2. Final opinion
KSPCB CFO renewal fee should be treated as GST-exempt under Sl. No. 4 of Notification No. 12/2017-CT(R), and RCM should not be discharged.
KSPCB is a statutory Pollution Control Board constituted under the Water (Prevention and Control of Pollution) Act, 1974, and is therefore not synonymous with the State Government for purposes of Sl. No. 5 of Notification No. 13/2017-CT(R).
Sl. No. 4 of Notification 12/2017 exempts services by a governmental authority by way of activities relating to functions entrusted to a Municipality under Article 243W. The relevant constitutional function includes "protection of the environment and promotion of ecological aspects." KSPCB's statutory functions of pollution prevention/control and grant of statutory consent are directly connected with this environmental function. (CBIC GST)
Accordingly, the better view is:
CFO renewal fee paid to KSPCB is exempt under Sl. No. 4 of Notification No. 12/2017-CT(R); RCM under Sl. No. 5 of Notification No. 13/2017-CT(R) is not applicable.
Documentation
The fact that KSPCB issues only an online payment receipt and not a GST tax invoice does not create an RCM liability. The company should retain:
KSPCB online payment receipt;
CFO renewal application/order;
fee calculation/challan;
applicable KSPCB fee notification/rate schedule; and
a brief GST exemption note citing Sl. No. 4 and the Article 243W environmental function.
No self-invoice, payment voucher or RCM payment should be required where the underlying service is exempt.
Important qualification
The exemption should be documented as Sl. No. 4 exemption based on KSPCB's governmental-authority status and the environmental function nexus, rather than on the proposition that CFO is merely a "registration".
Conclusion: GST payable under RCM - NO. GST exemption under Sl. No. 4 - YES, subject to the above statutory nexus and verification for the relevant tax period.