"Gupta submitted his resignation yesterday and the same will be processed by the government," a source said.
He was the coal secretary between 2006 and 2009, the period which is under the scanner of the CBI for alleged irregularities in allocation of coal blocks.
Gupta has been a member of fair trade regulator Competition Commission of India (CCI) since 2009 and his tenure was to end to early next year.
The corporate affairs ministry, the administrative ministry for the CCI, had earlier refused to grant permission to CBI to question Gupta.
During the 2006-09 period, 68 coal blocks were alloted to 151 companies and files of some of them had gone missing.
CBI, which is probing the coal block allocation scam, has registered 12 FIRs related to alleged irregularities in the allotment coal blocks between 2006 and 2009.