The Central Board of Indirect Taxes and Customs (CBIC) has confirmed that GST Audit will still apply for the financial year 2019-20. Although the Union Budget 2021 proposed amendments to the GST Act that would remove GST Audit, these changes will only take effect from a date to be notified later. Therefore, for the financial year 2019-20, the current rules remain in place.
The Union Budget 2021 has scrapped GST Audit as Section 35(5) has been committed from the GST Act. In this regard, several taxpayers and professionals were confused whether GST Audit will be applicable for FY 2019-20. CBIC, via their official Twitter handle, has clarified that GST Audit will be applicable for FY 19-20. Read the official Tweet below:
CBIC notifies that Sections 35 and 44 of CGST Act are proposed to be amended in Finance Bill 2021.
However, these proposals will come into effect from a date to be notified later.
For FY 2019-20, the existing provisions shall continue.

FAQ :
Yes, the CBIC has clarified that GST Audit will be applicable for FY 2019-20.
The Union Budget 2021 proposed to scrap GST Audit by amending Section 35(5) of the GST Act, leading to confusion among taxpayers and professionals.
The proposed amendments to Sections 35 and 44 of the CGST Act, which would scrap GST Audit, will come into effect from a date to be notified later.
For FY 2019-20, the existing provisions of the GST Act will continue to apply.
The Central Board of Indirect Taxes and Customs (CBIC) clarified the situation via their official Twitter handle.