Mallya called for more "transparency" and "inclusive approach" in the administration of the Indian Premier League.
The Mumbai Indians had shot a letter to the IPL governing council, asking why the auction was changed from "selection of sets at random" to pre-decided "order of auction list" for the January 8-9 players auction.
"I agree with the Mumbai Indians letter that there got to be more transparency and more inclusive approach were franchises, who are the principal stakeholders in the IPL, should be taken into confidence and consulted on policy matters," Mallya told Times Now.
"The Mumbai Indians questioned the process on which the players were categorised into various groups in the auction and I agree with that," he added.
The liquor-baron said he hoped in the future the IPL "I look forward to clarification from the IPL or response to Mumbai Indians letter. I have further gone on records to say that I wish there would be an inclusive process, where the franchise, the principal stakeholders, would also be given a greater consultative role in the entire IPL administration process," he said.
Nikhil Meswani, executive director of Reliance Industries, had written a letter to the IPL Governing Council, saying there was "no justification" for the last-minute change of auction rules.
The IPL franchises were informed about the last minute change by the Governing Council Jan 7, just a day before the auction.
Suspended Indian Premier League (IPL) chairman Lalit Modi also questioned the last-minute changes made to the January 8-9 players' auction in Bangalore on Friday.