If you've applied for a GST refund and received a notice labeled RFN-06, it means the GST officer has either found deficiencies in your refund application or has formally rejected it. This notice is issued under Rule 90 and Rule 92 of the CGST Rules, 2017, and must be responded to promptly to protect your refund claim. Taxocity's GST compliance experts have helped thousands of businesses navigate GST refund rejections since our inception over three decades ago, with a 4.8/5 rating from 5,000+ clients.

• RFN-06 can be a deficiency memo (under Rule 90) or a rejection order (under Rule 92)
• You typically have 15 days to rectify deficiencies after receiving a deficiency memo
• A refund rejection order can be appealed before the Appellate Authority within 3 months of the order date

What is RFN-06 in GST?

RFN-06 is an official reference number format used on the GST portal for two distinct actions taken by a proper officer on a refund application:

1. Deficiency Memo - Issued under Rule 90(3) of the CGST Rules, 2017, when the refund application is found to be incomplete or deficient in documents or information.
2. Rejection Order - Issued under Rule 92(1) of the CGST Rules, 2017, when the proper officer, after due process, is satisfied that the refund claim is not admissible wholly or in part.

Both communications are generated on the GST common portal (www.gst.gov.in) and are accessible in your dashboard under the "Refunds" section. It is important not to confuse the two as the actions you must take and timelines differ significantly between them.

RFN-06 Deficiency Memo: Rule 90(3)

When you file a GST refund application using Form RFD-01, the proper officer is required to examine the claim within 15 days of filing. If the officer finds any deficiency, they must communicate it through a deficiency memo (RFN-06) before rejecting the claim outright.

Common Reasons for a Deficiency Memo

• Incorrect or mismatched GSTIN of the applicant or supplier
• Missing supporting documents such as invoices, shipping bills, or bank realization certificates (BRC/FIRC)
• Discrepancy between GSTR-1, GSTR-3B, and the refund claim amount
• Incorrect category of refund selected (e.g., selecting "export of goods" instead of "export of services")
• LUT/Bond not filed or not linked to the refund application
• Incomplete Statement 3/3A for export-related refunds
• Declaration in Form RFD-01 not matching the actual facts
• HSN/SAC codes incorrectly mentioned on invoices

How to Respond to a Deficiency Memo

Upon receiving a deficiency memo under Rule 90(3), the original refund application is treated as not filed. This means you must file a fresh refund application after rectifying all the deficiencies mentioned in the RFN-06 notice. The steps to be followed are:

1. Log in to the GST portal and navigate to Services > Refunds > Track Application Status
2. Download and carefully read the RFN-06 deficiency memo
3. Identify all the deficiencies listed by the officer
4. Gather or correct the required documents and information
5. File a fresh Form RFD-01 with the corrected information and complete documents
6. Ensure the refund application references the original ARN if required

Note: The original ARN (Application Reference Number) is cancelled on issuance of the deficiency memo. A new ARN is generated upon re-filing, and the time limit for refund processing restarts from the new filing date.

RFN-06 Rejection Order: Rule 92(1)

A rejection order under Rule 92(1) is a more serious action. It is issued only after the proper officer has given you a show cause notice (SCN) in Form RFD-08 and considered your reply (filed in Form RFD-09). If the officer remains unsatisfied, a formal rejection order is issued in the prescribed format, which may be communicated as an RFN-06 order on the portal.

Grounds for Refund Rejection

Ground	Relevant Provision
Refund claim not admissible under Section 54 of CGST Act	Section 54, CGST Act 2017
Exports not proved through shipping bills or FIRC/BRC	Rule 89(2)(b)/(c), CGST Rules
ITC wrongly availed and reversed not eligible for refund	Section 54(3), CGST Act
Inverted duty structure refund not satisfying conditions	Section 54(3)(ii), CGST Act
Refund already granted/adjusted against demand	Section 54(10), CGST Act
Time limit of 2 years from relevant date exceeded	Section 54(1), CGST Act

How to Respond to a Rejection Order

If you receive an RFN-06 rejection order, the proper recourse is to file an appeal before the Appellate Authority under Section 107 of the CGST Act, 2017. The timeline and process are as follows:

1. File Form GST APL-01 (appeal application) within 3 months from the date of the rejection order
2. The Appellate Authority may condone a delay of up to 1 month if sufficient cause is shown
3. A pre-deposit of 10% of the disputed refund amount is required before admission of the appeal (as applicable under Section 107(6))
4. Submit all relevant evidence, invoices, export documents, and legal arguments along with the appeal
5. Attend the hearing and present your case or authorize a GST practitioner/CA to appear on your behalf

Deficiency Memo vs. Rejection Order: Key Differences

Parameter	Deficiency Memo (Rule 90)	Rejection Order (Rule 92)
Stage of issuance	Before processing begins (within 15 days of filing)	After SCN and reply process
Form / Reference	RFN-06 (Deficiency Memo)	RFN-06 (Rejection Order)
Effect on application	Original application treated as not filed	Refund claim formally denied
Taxpayer action required	File fresh RFD-01 after rectification	File appeal in GST APL-01
Time limit for action	No prescribed limit but act promptly within original 2-year window	3 months from date of rejection order
Pre-deposit required?	No	Yes (10% of disputed amount)

Important Timelines to Remember

• 2 years from the "relevant date" to file a GST refund application under Section 54(1) of the CGST Act, 2017
• 15 days for the officer to issue a deficiency memo after receiving your application
• 60 days is the prescribed processing time for granting refunds under Section 54(7)
• 3 months to file an appeal against a rejection order under Section 107(1)
• Interest at 6% per annum is payable by the government if refund is delayed beyond 60 days (Section 56)

Common Mistakes That Lead to RFN-06

Most RFN-06 deficiency memos and rejection orders can be avoided with careful preparation. Here are the most frequent errors businesses make when filing GST refund applications:

• Not reconciling GSTR-1, GSTR-3B, and ICEGATE data before filing the refund for export cases
• Failure to upload the correct Statement 3 for zero-rated supply refunds
• Uploading documents in unsupported file formats on the GST portal
• Claiming refund of ITC that has already been reversed in GSTR-3B
• Not linking the correct tax period with the refund claim
• Filing under the wrong refund category on Form RFD-01
• Not filing a fresh LUT for the relevant financial year before claiming IGST exemption on exports

How Taxocity Helps with GST Refund Issues

Taxocity has been helping Indian businesses with GST compliance for over three decades. Our team of real human GST experts provides end-to-end support, from filing the initial refund application to representing you in refund rejection appeals before the Appellate Authority.

Our 100% compliance guarantee means that every document is verified, every timeline is tracked, and every communication from the GST portal is addressed on time. Whether you have received an RFN-06 deficiency memo or a rejection order, our experts help you assess the officer's grounds, prepare the strongest possible response, and file the necessary forms without delay.

Our GST Refund Support Includes

• Review of your original refund application and identification of deficiencies
• Preparation and filing of a fresh RFD-01 with corrected data and complete documentation
• Drafting a reply to the SCN in Form RFD-09 with legal arguments and evidence
• Filing and pursuing your appeal in Form GST APL-01 before the Appellate Authority
• Reconciliation of GSTR-1, GSTR-3B, and export records to prevent future rejections

Explore our GST Filing services and GST Registration support for end-to-end GST compliance. If you've received a notice related to discrepancies in your GST returns, read our guide on responding to a GST scrutiny notice or our article on handling a GST show cause notice.

Key Takeaways

1. RFN-06 is a GST portal reference for both a deficiency memo (Rule 90) and a rejection order (Rule 92).
2. A deficiency memo means your application is treated as not filed; you must re-file with corrections.
3. A rejection order requires filing an appeal in GST APL-01 within 3 months.
4. Most RFN-06 notices arise from document mismatches, wrong refund category selection, or ITC reconciliation errors.
5. Act quickly because the 2-year time limit for refund claims continues to run even after a deficiency memo.
6. Interest at 6% p.a. is your right if the refund is delayed beyond 60 days by the department.

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Disclaimer: This article is for general informational purposes only and does not constitute tax or legal advice. GST laws and rules are subject to amendment by the government. Please consult a qualified tax advisor or GST practitioner before taking any action on a refund matter. Taxocity's experts are available to provide personalized guidance specific to your situation.