🧾 Cross-Empowerment under GST: One Authority, One Proceeding — How to Handle Partial Overlaps

💡 Introduction

When the Goods and Services Tax (GST) was introduced, the dream was “One Nation, One Tax.”Yet, in real practice, taxpayers often face two sets of proceedings — one from CGST authorities and another from SGST authorities — sometimes on the same transactions.

In certain cases, both departments raise identical points; in others, the notices overlap partially with some new observations.This creates a practical dilemma:

“Can two authorities proceed on the same issue — even partly — or does Section 6 of the CGST Act prevent it?”

Let’s decode the law, the administrative instruction, and how professionals should respond in such mixed situations.

⚖️ Statutory Foundation — Section 6 of the CGST Act

Section 6(1) – Cross-Empowerment Built-In

It empowers officers of one wing (Central or State) to act as “proper officers” for the other, ensuring smooth and uniform enforcement.

“Officers appointed under the State Goods and Services Tax Act are authorised to be proper officers for the purposes of this Act…”

Hence, no separate notification is required for cross-empowerment — it is automatic.

Section 6(2)(b) – The Guardrail Against Duplication

“Where a proper officer under the State GST Act has initiated any proceedings on a subject matter, no proceedings shall be initiated by the proper officer under this Act on the same subject matter.”

This provision is the heart of protection for taxpayers — it prevents the same subject matter from being litigated twice by different wings.

🔍 The Core Issue: When Only Part of the Notice Overlaps

In practice, proceedings may fall into three categories:

Type	Description	Legal Position
Full overlap	CGST & SGST notices are for the same facts, same period, same grounds.	Second notice must be dropped completely under Section 6(2)(b).
Partial overlap	Some issues are identical, others are new or distinct.	The overlapping portion must be withdrawn, while new issues can proceed.
Distinct issues	Completely separate causes of action.	Both notices valid if no factual duplication.

It’s this second category — partial overlap — that creates confusion.

🧩 Practical Example

A registered dealer receives an SCN from the SGST department covering three issues:

1. ITC reversal on ineligible purchases

2. Under-reported rental income

3. ITC on motor-vehicle expenses

Later, the CGST department issues another SCN covering:

1. ITC reversal on ineligible purchases (same issue)

2. Wrong classification of goods (new issue)

Here, the first issue overlaps, but the second one doesn’t.The taxpayer must protect themselves from duplication without blocking the valid new proceeding.

🧾 Instruction No. 01/2023-24-GST (Inv.), dated 30 March 2024

Recognising the chaos of parallel proceedings, the Directorate General of GST Intelligence (DGGI) issued this instruction.

Key directions:

• Before initiating any investigation or notice, the officer must ascertain whether another authority has already initiated a proceeding for the same subject matter.

• If overlap exists, the matter should be referred to the approving authority for coordination and rationalisation.

• Departments are expected to maintain inter-authority communication to prevent taxpayers from receiving duplicate SCNs.

This instruction provides a procedural remedy and supports a taxpayer’s objection if duplication still occurs.

✍️ How to Respond — Draft Representation Letter

Below is a model letter that can be filed before the second authority (CGST/SGST) to seek withdrawal of overlapping issues while cooperating on the remaining matters.

Sample Representation Letter

ToThe Officer

[Designation & Office Address]

[Department Name – CGST / SGST]

Date: 

Subject: Representation under Section 6(2)(b) of the CGST Act – Overlapping Proceedings with [State/Central] GST Office

Respected Sir / Madam,

We refer to the Show Cause Notice No. ____ dated ____ issued by your office.We wish to respectfully submit that certain issues covered in the said notice are already the subject matter of proceedings initiated by the [State/Central] GST department vide Notice No. ____ dated ____.

A comparison of both notices reveals partial overlap as per the table below:

Sl. No.	Issue / Observation	Period Covered	Covered in Earlier Notice (Yes/No)	Remarks
1	Input-tax credit reversal on ineligible invoices	Apr 2022 – Mar 2023	Yes	Same invoices and grounds
2	ITC on motor vehicle expenses	Apr 2022 – Mar 2023	No	New issue
3	Short-payment of tax on rent income	Apr 2022 – Jun 2022	Yes	Identical subject matter

1. Statutory bar under Section 6(2)(b)

Section 6(2)(b) clearly prohibits a second proceeding on the same subject matter once a proceeding is initiated by the counterpart authority.Therefore, items 1 and 3 above fall squarely within the bar.

2. Administrative Instruction dated 30 March 2024

As per Instruction No. 01/2023-24-GST (Inv.), the department must ensure that no parallel or overlapping proceedings are initiated.The duplication evident in the present case appears contrary to this instruction.

3. Request

We humbly request that:

1. The issues already under adjudication before [Name of other department] be dropped from this notice in terms of Section 6(2)(b); and

2. The remaining independent issues be adjudicated separately, for which we shall provide full details and supporting documents.

This approach will avoid duplication and align with the cooperative federalism envisioned under GST.

Yours faithfully,

🧠 Professional Guidance for Practitioners

Step	Action	Why It Matters
1	Identify and segregate issues — identical vs. distinct.	Only identical issues fall under Section 6(2)(b).
2	Respond in writing before due date citing Section 6(2)(b).	Creates a record of your objection.
3	Attach copy of earlier notice and comparison table.	Proves overlap objectively.
4	Refer to Instruction 01/2023-24-GST (Inv.).	Strengthens procedural argument.
5	If authority refuses to drop overlapping issues, approach High Court via writ petition.	Courts have repeatedly upheld the bar against duplicate SCNs.

🧾 Conclusion

Cross-empowerment under Section 6(1) ensures administrative flexibility;Section 6(2)(b) ensures fairness by preventing duplication.

When some issues overlap and others don’t, the solution lies in segregation, not duplication.Taxpayers should assert their rights calmly and clearly, while cooperating on distinct matters.

One Law, One Nation — and One Proceeding.The GST framework was designed for coordination, not competition between departments.