The May 16 arrest of three cricketers, including former test bowler Shanthakumaran Sreesanth, has exposed Indian cricket's soft underbelly.
The trio have denied allegations they took money from bookmakers to concede a pre-determined number of runs in IPL matches but their arrest has prompted Indian police to launch raids for illegal bookmakers across the country.
"I have sent my resignation to the BCCI (Indian cricket board) president," Shukla told reporters, adding he had made up his mind earlier this week not to continue in the post.
Shukla, a junior union minister, is the third official to quit after BCCI secretary Sanjay Jagdale and treasurer Ajay Shirke stepped down on Friday.
The BCCI's working committee will meet in Chennai on Sunday with intense pressure on board president N. Srinivasan to quit after his son-in-law and IPL Chennai franchise official Gurunath Meiyappan was arrested last month as part of the investigation.