Common Questions About GSTR-9 Annual Return Filing

The Goods and Services Tax Return 9 (GSTR-9) is an annual filing required from most registered GST taxpayers. This return consolidates information on outward and inward supplies, tax obligations, and input tax credit utilized over a financial year. The standard deadline for GSTR-9 submission is December 31st of the year following the financial year. Historically, deadlines for the initial financial years were frequently extended.

Recent Updates on GSTR-9 Filing

The 55th GST Council convened in Jaisalmer, Rajasthan, on December 21, 2024. Key recommendations included issuing a circular to clarify late fees under Section 47(2) of the CGST Act, 2017, for delayed GSTR-9 and GSTR-9C submissions. Additionally, a notification will waive late fees for GSTR-9C submissions from 2017-18 to 2022-23. Further details are available here.

During the 53rd GST Council meeting, a recommendation was made to exempt taxpayers with an aggregate annual turnover below Rs. 2 crore from filing GSTR-9/9A for Fiscal Year 2023-24. This exemption was formalized through CGST Notification 14/2024, issued on July 10, 2024.

GSTR-9: Frequently Asked Questions

1. What is GSTR-9 and who is required to file it?

GSTR-9 is an annual return to be filed by all GST-registered taxpayers, irrespective of their entity's turnover. It encompasses details such as inward and outward supplies, taxes paid, refunds claimed, demands raised, and input tax credit (ITC) utilized. All registered taxpayers must file GSTR-9, with specific exceptions.

Exempted entities include:

• Casual taxpayers
• Input Service Distributors
• Non-resident taxpayers
• Taxpayers deducting or collecting tax at source under Section 51 or Section 52

Note: Composition scheme taxpayers file GSTR-4.

2. What are the consequences of not filing GSTR-9?

Failure to file GSTR-9 may result in a notice from the tax department and the imposition of late fees or penalties for non-compliance.

3. Which entities are exempt from filing GSTR-9?

The following categories of taxpayers are not required to file GSTR-9:

• Composition scheme taxpayers
• Casual Taxable Persons
• Non-resident taxable persons
• Input service distributors
• Individuals paying TDS under the CGST Act
• Individuals collecting TCS under the CGST Act

Furthermore, for financial years 2017-18 onwards, GSTR-9 filing was made optional for small businesses with a turnover under Rs 2 crore.

4. Is the HSN-wise summary mandatory in GSTR-9?

No, reporting the HSN code in GSTR-9 is optional.

5. How should ITC reversals be reported in GSTR-9?

Input Tax Credit (ITC) reversals must be declared in Table 7 of GSTR-9. Additionally, any ITC claimed during the previous financial year and reversed before November 30th of the subsequent year should be reported in Table 12 of GSTR-9.

6. How can additional tax liability be paid in GSTR-9?

To settle any additional tax liability identified in GSTR-9, taxpayers should use DRC-03.

7. Can amendments be made to GSTR-9?

Changes to GSTR-9 are permitted until the return is submitted. However, once submitted, GSTR-9 cannot be modified.

8. How is differential tax paid in GSTR-9?

Differential tax discovered in GSTR-9 can be paid using form DRC-03.

9. Can a composition dealer file GSTR-9?

No, a composition dealer is not eligible to file GSTR-9. Instead, they must file their annual return using GSTR-4 by April 30th of the following financial year.

10. What are the annual return implications when a business shifts between Regular and Composition Schemes within the same financial year?

When a business transitions between the Regular and Composition Schemes within a financial year, turnover and purchases must be separated as follows:

• Regular Scheme Turnover: Turnover from the period when the assessee was registered under the Regular Scheme must be reported in GSTR-9.
• Composition Scheme Turnover: Turnover from the period when the assessee was registered under the Composition Scheme must be reported in GSTR-4.
• Segregation of Purchases: Purchases made during the Regular Scheme registration period should be computed and reported in GSTR-9 to claim ITC. However, ITC cannot be claimed on purchases made while registered under the Composition Scheme.

11. If CGST, SGST, and IGST were incorrectly interchanged in GSTR-1, but the total tax value matches, can this be corrected in GSTR-9?

Errors where CGST, SGST, and IGST were interchanged in GSTR-1 cannot be rectified when filing GSTR-9. While Table 9, which details taxes paid in GSTR-9, allows editing only the 'tax payable' column, assessees can correctly report the actual taxes due under the appropriate heads. However, this accurate reporting does not automatically adjust taxes between CGST, SGST, and IGST. Any tax shortfall must be paid when filing the GSTR-3B of the subsequent month or by submitting DRC-03. Excess taxes erroneously paid can be claimed as a refund, and no interest liability arises for such short-paid taxes.

12. How should sales originally reported as B2C in GSTR-1, but later corrected to B2B, be declared?

Table 4 of GSTR-9 requires details for both B2B and B2C supplies. In this scenario, the assessee must report the sales under B2B in Table 4, reflecting the correct classification, even if it was mistakenly declared as B2C in GSTR-1.

13. If GSTR-3B was filed with incorrect (excess) outward supplies and tax paid on them, but the correct supplies were declared in GSTR-1 for the same period, is there a way to obtain a refund for the excess payment?

If taxes were erroneously overpaid in GSTR-3B, the excess amount can be claimed as a refund under Section 54 of the CGST Act or adjusted against future tax payments. This refund cannot be claimed through GSTR-9. A separate application for refund must be submitted on the GST portal.

14. Should sales originally reported as “With payment of taxes” but later corrected to “Without payment of Taxes” be reported in Table 4C?

Since the correct nature of sales, in this case, is without tax payment, they should be reported in Table 5A of GSTR-9, not Table 4C. GSTR-9 requires accurate reporting, regardless of prior incorrect declarations in GSTR-1 as 'With payment of taxes'.

15. If a LUT was not executed, and sales were reported as “Without Payment of Taxes,” should these now be treated as Exports with payment of Taxes?

Failure to execute a Letter of Undertaking (LUT) is a procedural non-compliance and does not change a transaction's nature from 'exports without payment of tax' to 'exports with payment of tax'. The taxpayer should report the transaction under Table 5 of GSTR-9 as "Exports without payment of tax." Any potential penalties for non-compliance must be addressed separately.

16. How should an advance received in 2017-18, with an invoice issued in 2017-18, but belatedly reported in GSTR-1 in FY 2018-19, be handled in Table 4F?

This transaction should be reported in Table 4A (for supplies to unregistered persons) or Table 4B (for supplies to registered persons). Reporting under Table 4F is only applicable when tax on advances has been paid but the invoice has not yet been issued.

17. If Reverse Charge was paid but wrongly reported in GSTR-3B under 3.1.a instead of 3.1.d, how can this be corrected when filing GSTR-9?

The assessee should accurately report the reverse charge paid under Table 4G of GSTR-9, even if it was incorrectly reported in GSTR-3B.

18. Can a refund be claimed for credit notes pertaining to FY 2017-18 that could not be adjusted in FY 2018-19?

No, a refund for credit notes related to FY 2017-18 that could not be adjusted in FY 2018-19 cannot be claimed, as the tax incidence on such supply has already been passed to the recipient.

19. Can GSTR-3B values be used for GSTR-9 filing? Which tables are uneditable?

Yes, values from GSTR-3B can be used for GSTR-9 filing. Taxpayers can edit auto-populated data from GSTR-3B, except for Table No. 6A, which shows the total ITC availed.

20. Can new credit not claimed in GSTR-3B filings be reported in GSTR-9?

No additional credit that was not claimed in GSTR-3B can be claimed in GSTR-9. However, credit claimed in a filed TRAN-1 can be reported in GSTR-9 under Table 6K/6L or Table 13, as appropriate.

21. What are the implications of GSTR-9 filing with a deviation of over 20% in values (e.g., ITC difference between claimed and GSTR-2A)?

Most GSTR-9 tables are auto-populated from GSTR-1 and GSTR-3B. Taxpayers can edit these values, but a difference exceeding 20% will highlight the cells in red and prompt a confirmation message. GST authorities may issue a notice requesting reconciliation of ITC claimed in GSTR-3B and the system-generated GSTR-2A. Any differential tax amount may need to be paid.

22. How is a discrepancy between GSTR-3B and GSTR-2A rectified in GSTR-9?

Differences between auto-populated ITC details from GSTR-2A and those declared in GSTR-3B should be explained in GSTR-9 under two categories:

• Table 8E: ITC available but not availed
• Table 8F: ITC available but ineligible

23. If ITC reversals were missed in past GSTR-3B filings, how should they be handled in GSTR-9?

Missed ITC reversals from previous months' GSTR-3B can be performed in subsequent GSTR-3B filings. These should be accurately reported in Table 7 of GSTR-9, and any resulting excess liability must be paid.

24. How should ITC be bifurcated into Capital Goods, Inputs, and Input Services?

Table 6B of GSTR-9 mandates the bifurcation of ITC into Capital goods, Inputs, and Input Services. Books of accounts should ideally be maintained to identify purchases attributable to output supply of goods, output services, and capital goods for ITC differentiation. However, as there is no difference in ITC treatment between goods and services, this bifurcation might be waived for the first year if the assessee's books were not maintained in the required manner due to prior non-requirement in GSTR-3B.

25. How are missing outward supply details from the previous financial year's GSTR-3B shown in the current financial year?

Missing outward supply details from the previous financial year's GSTR-3B should be correctly reported in Table 10 of GSTR-9. These details should be net of any credit or debit notes.

26. In Table 13, is the Input Tax Credit availed for 2017-18 asked net of reversal?

Table 13 requires details of ITC on goods or services received in the previous financial year but availed in the current financial year. Therefore, only ITC claimed in the current year but pertaining to the prior year needs to be reflected in Table 13, and this does not include any reversals.

27. Can wrongly claimed input tax credit in GSTR-3B be rectified in GSTR-9?

Excess credit claimed in GSTR-3B can be reversed by reporting the amount in Table 4(B)2 of a subsequent month's GSTR-3B. This can also be disclosed in Part V, Point 12 of GSTR-9.

28. Are stock transfers and cross charges within the same PAN included in aggregate turnover?

Yes, stock transfers and cross charges under the same Permanent Account Number (PAN) are included in aggregate turnover. As per Section 2(6) of the CGST Act, aggregate turnover encompasses "inter-state supplies of persons having same PAN."

29. What are the implications of improper HSN and SAC code reporting?

HSN (Harmonized System of Nomenclature) and SAC (Service Accounting Code) are standardized codes linked to GST rates. When filing an annual return, taxpayers select the HSN code, and the system automatically determines the applicable rate. Incorrect HSN code selection can lead to varying tax liabilities. Furthermore, Section 31 requires HSN for goods and services on invoices for ITC claims. Thus, furnishing an incorrect HSN code can impact the buyer's input tax credit eligibility.

30. What happens if the supplier files GSTR-1 after the recipient files GSTR-9?

If the recipient has filed GSTR-9 before the supplier files GSTR-1, the invoice details will be reflected for the supplier in GSTR-1A. The supplier must accept these invoices when filing their return. Only after acceptance can the recipient taxpayer claim ITC on those invoices.

31. What are the complexities of filing GSTR-9 for various sectors?

Various sectors face specific complexities when filing GSTR-9:

1. ITC Bifurcation: GSTR-9 now requires bifurcation of inputs, input services, and capital goods, which was not mandatory in GSTR-3B.
2. Demands and Refunds: Table 15 of GSTR-9 necessitates details of demands and refunds for FY 2017-2018. This requires taxpayers to categorize refunds by applied, sanctioned, rejected, and pending statuses, along with paid and pending demands.
3. HSN-wise Summary: An HSN-wise summary of inward supplies is required in GSTR-9, often necessitating extensive review of accounting records.
4. Supplies from Composition Dealers: Table 16A requires separate reporting of supplies from Composition dealers. Difficulties may arise if vendor master data does not categorize dealers by scheme.
5. Deemed Supply under Section 143: Table 16B requests details of deemed supplies under Section 143 (inputs and capital goods sent to job workers but not returned within the specified timeframe). Taxpayers who have not maintained this data will find it challenging to compile.
6. ITC Reversals: Table 7 requires details of reversals made under Rule 37, 39, 42, 43, and Section 17(5) when filing GSTR-3B. If a taxpayer missed reporting this in GSTR-3B and now wishes to reverse, it may not be possible.
7. GSTR-2A Auto-population: Table 8 automatically populates data from GSTR-2A. If a supplier has not filed GSTR-1 or paid taxes, the ITC will not appear in the recipient's GSTR-2A, requiring frequent follow-ups with suppliers.

32. How can credit from GST TRAN-1 be claimed if not already done?

The government extended the deadline for submitting declarations in Form GST TRAN-1 until March 31, 2019, for registered persons who encountered technical difficulties on the common portal and whose cases were recommended by the Council. Such assessees could claim credit from the earlier tax regime by submitting TRAN-1 before the extended due date.

33. If TRAN-1 or TRAN-2 filing is pending, must it be filed before GSTR-9?

Details of credit availed in TRAN-1 and TRAN-2 are to be reported under Table 6K and 6L of GSTR-9, respectively. Although the GST Rules initially set the GSTR-9 due date as December 31, 2018, the government extended it to June 30, 2019. Thus, GSTR-9 can be filed after submitting transition returns for FY 2017-2018. However, in this scenario, credit from TRAN-1 and TRAN-2 should not be disclosed in 6K and 6L of GSTR-9, as the amount is credited in the month the transition returns were filed.

34. What are the eligibility criteria for filing a “NIL” GSTR-9 return?

A NIL GSTR-9 annual return can be filed only if all the following conditions are met for that financial year:

• No outward supply was made.
• No goods or services were received.
• No other liability to report exists.
• No credit was claimed.
• No refund was claimed.
• No demand order was received.
• No late fees are due.

35. Table 5F requests inclusion of "no supply" in Non-GST supply. What does "no supply" entail, and does it include Schedule III transactions?

The term 'no supply' refers to activities or transactions that are neither a supply of goods nor a supply of services, as outlined in Section 7(2) of the CGST Act. This includes:

• Activities or transactions specified in Schedule III.
• Activities undertaken by Government or Local authorities in their capacity as public authorities.

36. In Table 15, when completing details of total refunds, should only refunds applied for in 2017-18 be included, or also those for 2017-18 applied in a subsequent financial year?

GST refunds claimed between July 2017 and March 2018 should be reported in Table 15A. If the refund was sanctioned after March 31, 2018, it is not reported in Table 15B. The cutoff date for reporting transactions under Table 15 is March 31, 2018.

37. Can taxpayers manually edit auto-populated fields in GSTR-9?

Yes, manual edits can be made to auto-populated details in GSTR-9, with the exception of the following tables:

• Table No. 6A: Total amount of input tax credit availed through GSTR-3B.
• Table No. 8A: ITC as per GSTR-2A.
• Table No. 9: Details of tax paid, excluding the tax payable column.

38. Is GSTR-9 required if registration was canceled before March 31, 2018?

According to Section 44(1) of the CGST Act, every registered person must file GSTR-9. Therefore, even if a taxpayer's registration status was unregistered as of March 31, 2018, but they were registered at any point between July 2017 and March 2018, they must file GSTR-9 for the period during which they were registered.

39. What are the similarities between GSTR-9A and GSTR-9C?

There are no similarities between GSTR-9A and GSTR-9C. GSTR-9A is the annual return form for Composition Dealers, while GSTR-9C is a reconciliation statement comparing GSTR-9 with annual audited financial statements.

40. What is the distinction between GSTR-9 and GSTR-9C?

GSTR-9 is an annual GST return that registered taxpayers under the Regular Scheme (monthly/quarterly) must file once a year. GSTR-9C serves as a reconciliation statement between GSTR-9 and the audited books of accounts.

41. How can an overpayment of GST on the same invoice be corrected or claimed?

If GST has been paid twice on the same invoice, the excess tax amount can be adjusted when filing the subsequent month's GSTR-3B.

42. When B2C and B2B supplies are amended by adding to B2B and reducing B2C, should the net amendment effect (zero) be disclosed, or both positive and negative entries?

For B2C transactions, there will be a net-off impact. However, for B2B, both the original invoice and any amendments must be shown separately.

43. If a taxpayer has 27 branches across India, is GSTR-9C required for all branches?

The aggregate turnover at the PAN level must be checked. If the annual turnover exceeds Rs 5 crore, GSTR-9C must be filed GSTIN-wise for the specific PAN. Note: The limit for GSTR-9C was increased to Rs 5 crore for FY 2018-19 through FY 2022-23 via CBIC notifications.

44. Is it mandatory to provide HSN codes for turnover below Rs 1.5 crore?

No, providing HSN codes is not mandatory for a turnover below Rs 1.5 crore.

45. Where should invoices pertaining to FY 2017-18 that were not uploaded previously be declared now?

These invoices can be declared in a subsequent GSTR-1 filing.

46. If there is a mistake in the reported taxable turnover of GSTR-3B, what is the rectification procedure?

The taxable turnover can be manually corrected in Form GSTR-9.

47. If taxes for missing invoices in FY 2018-19 were paid through GSTR-3B, where will this be reflected?

This will be reflected in the Electronic Cash Ledger.

48. If a dealer only had Non-GST sales, and figures were wrongly recorded and subsequently cancelled, must the total Non-GST sales amount be filed in the Annual Return?

Yes, the total amount of Non-GST sales must be disclosed in the annual return.

49. What if extra tax was paid? Is there a provision in GSTR-9, or should a refund be claimed?

GSTR-9 is a declaration form; no tax can be paid or refund generated through it. An overpayment of tax requires claiming a refund.

50. How should a transporter, whose services to a Private Limited Company fall under RCM, file their return if the company pays GST through RCM and the transporter does not pay GST?

The transporter must file their GSTR-1, reporting the transaction as B2B (Reverse Charge).

51. Are there possibilities for further extensions to the Annual Return filing deadline of June 30, 2019?

Currently, no notification regarding further extensions is available.

52. If Table 8 shows a negative balance other than for imports, what action should be taken?

Table 8 should not show negative values for anything other than imports from SEZs. Negative values can only occur if the value in Table 8C exceeds Table 8A, which indicates a discrepancy.

53. Can Non-GST turnover (e.g., Petrol, Alcohol) be shown in GSTR-9?

No, Non-GST turnover cannot be reported in GSTR-9.

54. A credit note for interstate sales returns was issued in March 2019, but no interstate supply was made in March 2019. How can the liability be adjusted in GSTR-3B?

The credit note from March 2019 must be carried forward to the April 2019 GSTR-3B, as the GSTN does not accept negative values.

55. If GSTR-3B data aligns with books of accounts, but a short amount was disclosed in GSTR-1, should the difference be shown in the amendment section?

Manual amendment data can be shown in Table 4 and 5 if it pertains to FY 2017-18. However, if the amendment for FY 2017-18 relates to FY 2018-19, it must be shown in Table 10 and 11. This could lead to a notice from the GST Department for not reflecting the amendment in GSTR-1 for the relevant period.

56. What are the methods for resolving warnings in GSTR-9 (e.g., differences between GSTR-3B and GSTR-1)?

There are no specific "hacks" for GSTR-9 warnings. It is crucial to ensure that all information reported in GSTR-9 is supported by proper documentation.

57. What turnover is considered for determining GSTR-9C applicability?

The turnover for GSTR-9C applicability is the turnover as per the entity's audited financial statements, compared with the turnover declared in GSTR-9.

58. What happens if a business files GSTR-9 but not GSTR-9C, and how will the government identify such taxpayers?

The GSTN already possesses records of turnover for a financial year through GSTR-1 and GSTR-3B filings. Based on these records, the authorities will issue notices to businesses that fail to file GSTR-9C when applicable.

59. Can GSTR-9 be amended?

No, GSTR-9 cannot be amended once filed.

60. If sales were not reported in GSTR-1 and GSTR-3B, how should they be disclosed in GSTR-9?

The GSTR-9 form allows manual editing of most fields, except for a few auto-calculated cells, enabling taxpayers to report previously undisclosed sales.

61. How important is the GSTR-1 versus Sales Register comparison for GSTR-9 filing, and what if there is a difference?

It is critical to reconcile any unreconciled differences between the Sales Register and GSTR-1 before filing GSTR-9, as GSTR-9 cannot be revised. Any discrepancies can be manually adjusted in GSTR-9.

62. If tax liability for FY 2017-18 was paid in March 2019, where should it be reported in GSTR-9?

This payment should be reported in Table 9 of GSTR-9.

63. How can GSTR-3B be filed without filing returns for previous months?

GSTR-3B for prior periods must be filed before submitting the return for the current month.

64. Are there updates for GSTR-9 regarding credit claimed after September 2018 and up until March 2019?

Yes, Input Tax Credit for FY 2017-18 can be claimed until March 2019 in the GSTR-3B return, and this can also be reflected in GSTR-9.

65. If GSTR-10 has already been filed, is GSTR-9 also required?

Taxpayers should check their GSTN login. If GSTR-9 appears there, it must be filed; otherwise, it is not required.

66. The system-generated GSTR-9 is available. Can it be filed without changes?

While a system-generated GSTR-9 can be filed, it is advisable to verify the auto-filled details before submission, as GSTR-9 cannot be revised. Additionally, some tables require manual completion.

67. The tax payable to date is not displayed anywhere. Can it be shown in Table 9?

The GSTN currently requires details of tax paid and declared during FY 2017-18 in Table 9 of GSTR-9.

68. If tax has been paid but GSTR-3B was submitted as a Nil return, how should the Annual Return be filed?

Manual changes can be made in GSTR-9 to reflect the tax paid.

69. In Table 15, if a refund application was made but not received by March 31, 2018, and received after this date, how should it be reported in GSTR-9? Is sanction required for refunds?

The GSTN has not provided clear guidance for refunds sanctioned after March 31, 2018, but pertaining to FY 2017-18. Sanctions are indeed required for refunds.

70. If there is a discrepancy in advances, can it be corrected in GSTR-9?

Yes, manual changes can be made in GSTR-9 to correct the advances value.

71. Is it mandatory to mention SAC Codes in GSTR-9 for Outward Supplies?

Yes, if your turnover exceeds Rs 1.5 crore.

72. Can sales shown as interstate sales be changed to export sales in GSTR-3B?

These changes can be made in GSTR-3B as it provides summary-level details.

73. If Cess was short-claimed in FY 2017-18 and then claimed in March 2019's GSTR-3B, can it be adjusted for FY 2017-18 when filing GSTR-9?

Yes, manual changes can be made in GSTR-9 for this adjustment.

74. If a purchaser made a purchase return in FY 2017-18, and the seller uploaded the credit notes in FY 2018-19, what is the treatment in GSTR-9?

This situation means the purchaser's GSTR-2A shows less input tax credit in FY 2018-19, having already reduced the ITC in FY 2017-18 in their GSTR-3B. The GSTN auto-pull will reflect the correct values in Table 6 of the purchaser's GSTR-9 when filed.

75. Where can missing sales bills be added in GSTR-1?

Missing sales bills can be added in the subsequent month or quarter's GSTR-1 filing.

76. If SGST was paid instead of IGST, must additional IGST payable be shown in Table 9?

Payment for IGST for FY 2017-18 must be made first, then declared in Table 9.

77. Will the portal accept negative figures in the GSTR-2A reconciliation table? For example, if the recipient has input tax credit but the supplier has not filed GSTR-1.

Table 8C will show negative values if Table 8A has a lower value compared to Table 8B and 8C. The portal will accept these negative values.

78. If turnover is below Rs 1.5 crore, can an auto-populated GSTR-9 form be filed?

While an auto-populated GSTR-9 form can be filed, it is important to check the auto-filled details before submission, as GSTR-9 cannot be revised, and some sections require manual completion.

79. Can transactions not reported earlier be declared in the GSTR-9 return? Can liability from such transactions be paid, or ITC claimed?

Yes, transactions undisclosed in 2017-18 GST returns can be reported when filing GSTR-9. Any resulting liability must be paid using Form DRC-03. However, no new input tax credit can be claimed. Examples include supplies made without consideration, goods sent on approval, or deemed supplies (e.g., goods sent to job workers not returned within specified times).

80. Can a taxpayer file their return using only the auto-populated data from GSTN in GSTR-9?

The GSTN auto-populates several GSTR-9 tables for convenience. However, this data is not necessarily accurate. Every taxpayer must verify this data against their books of accounts and filed GST returns. If discrepancies are found, the correct figures from books or GST returns should be reported in GSTR-9.

81. A taxpayer made a payment using Form DRC-03 in October 2017. Why is this payment not reflected in GSTR-9?

Payments made using Form DRC-03 from July 2017 to March 2018 will not be accounted for in GSTR-9. However, they must be reported in the reconciliation statement, Form GSTR-9C.