Deficiency memos in RFD-03 and the limitation reset problem

A memo is not a rejection, but it can cost you the claim entirely if the two year date is close.

The problem

A claim filed within time is met with a deficiency memo. The applicant cures the defect and refiles. By then the two year period has expired. The department rejects the fresh application as time barred.

The rules do not expressly preserve the original filing date, which is what creates the dispute.

The answer is that a defective application is still an application, that the rules cannot curtail a statutory entitlement, and that the department's own memo caused the delay. Courts have accepted variants of this reasoning, and the position should be pleaded rather than assumed.

How to avoid the problem entirely

File early in the two year window, not at the end of it. Most of these disputes exist only because the claim was filed in the final weeks.

Upload every document the rules mention, in the prescribed statement format, even where the portal permits the filing without them.

Where a memo issues, refile the same week. The delay between the memo and the fresh application is what the department relies on.

Keep the original ARN, the memo and the fresh ARN together, with dates, because that sequence is the whole case if limitation is argued.

When the memo is itself wrong

A memo issued for a document not prescribed by the rules is bad, and the reply should say so while still furnishing the document.

Repeated memos on the same application, each raising a new requirement, have been deprecated, and a written objection creates the record for a writ.

A memo issued after the acknowledgement in RFD-02 has been given is irregular, because the acknowledgement records completeness.

Where memos are used to defer a claim indefinitely, a writ for a direction to decide the application is effective and courts have awarded interest.

What to do on Monday

1. File refund claims in the first half of the two year window as a matter of policy.

2. Refile within a week of any deficiency memo, and record the dates.

3. Object in writing where a memo demands a document the rules do not prescribe.

4. Keep the ARN and memo chronology in the claim file; it is the limitation defence.

Questions we are asked on this

Does a deficiency memo mean the claim is rejected?

No. It means the application is treated as not filed and must be refiled after rectification.

Does the two year period stop when we file the first time?

The department says no. The taxpayer's argument is that a defective application is still an application and that the memo caused the delay. Plead it with the dates.

How quickly should we refile?

Within days. The gap is the department's best point.

Can a second memo be issued on the fresh application?

It happens, and it should be objected to in writing where the new requirement could have been raised in the first memo.

Is a memo appealable?

It is not an order rejecting the claim, so the practical remedies are refiling and, where memos are used to stall, a writ.

In this cluster

• GST refunds: every category, every form, every deadline
• Export refunds: the LUT route versus the IGST route
• VKC Footsteps: why input service tax stays stuck in an inverted duty structure
• Provisional refund of ninety percent: the mechanism and how to keep it
• Replying to RFD-08: the refund rejection notice
• Interest on delayed refunds under Section 56
• Unjust enrichment in GST refunds: when it applies, and when it does not
• Section 77: refund where tax was paid under the wrong head
• SEZ supplies and refund: endorsement, authorised operations and the disputes
• Deemed exports and the refund to the recipient

GST Insights is published by AMLEGALS for general information. Law stated as on 3 September 2026. Not advice on any particular set of facts; not an advertisement or a solicitation under Rule 36 of the Bar Council of India Rules. Readers with a question on their own facts may write to the GST practice of their own accord.