After senior Board officials such as IPL chairman Rajiv Shukla, vice-President Arun Jaitley and Jyotiraditya Scindia urged him to step aside, the Ministry has also sought his ouster.
"BCCI is inquiring into allegations of match and spot fixing. As there is a conflict of interest in this inquiry, therefore BCCI President should tender his resignation on moral grounds, pending the outcome of the inquiry," the Ministry said in a statement.
A three-member BCCI inquiry committee is also probing Meiyappan and the allegations against three Rajasthan Royals players and its franchise as well as the Chennai Super Kings.
Justice T Jayaram Chouta, former Judge of the Karnataka and Madras High Courts, Justice R Balasubramanian, former Judge of the Madras High Court, and BCCI Secretary Sanjay Jagdale are members of the Commission.
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The Ministry said it is observing the unfolding events "with considerable disquiet" and reiterated its commitment towards a strong anti-corruption law for sports.
The Ministry, meanwhile, rejected reports that it was in favour of legalising betting to curb corruption in sports.
"The Ministry of Sports has also observed that a section of the Media has reported that it is in favour of a law regularising betting in the sporting events in the country.