Delivering a keynote speech in London earlier this week, Botham said the IPL was "too powerful" for cricket's long-term good.
But Sanjay Patel, secretary of the Indian board (BCCI), said Friday that Botham was in no position to take the moral high ground after his involvement in disgraced Texas financier Allen Stanford's ill-fated T20 competition between the West Indies and England.
"I can still visualise the photo of Botham sitting in the front when Stanford went to England -- and he has the temerity to talk about IPL," Patel told the Press Trust of India news agency.
"We don't want his advice. We have enough top players like (former Indian players) Sunil Gavaskar, Ravi Shastri, Kapil Dev and Rahul Dravid to advise us."
Botham was one of several cricketing legends who appeared alongside Stanford at the 2008 launch of his competition which was cancelled after the first edition following allegations of fraud against the Texan.
Stanford was later sentenced to 110 years in prison for heading up a $7 billion Ponzi scheme in a verdict which was seen as a huge embarrassment for the England cricket board.
While few England players appear in the IPL, the annual tournament does feature star names from most of the Test-playing nations. Some have shunned the chance of playing for their country, opting instead to take the greater financial rewards on offer at the IPL.
"How on earth did the IPL own the best players in the world for two months a year and not pay a penny to the boards who brought these players into the game?" Botham said on Wednesday as he delivered the annual MCC Spirit of Cricket Cowdrey lecture at Lord's.
"I'm worried about the IPL. In fact, I fear it shouldn't be there at all. It is changing the priorities of world cricket."
But Patel said Botham had failed to "get his facts" right and that India had "distributed over $10 million as compensation to other cricket boards for allowing their players to play in the IPL".
The IPL is currently being investigated for match-fixing and corruption by India's Supreme Court.
International news organisations, including Agence France-Presse (AFP), have suspended their on-field coverage of matches hosted by the BCCI since 2012 after the board imposed restrictions on picture agencies.
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