"I don't think this administrative subject should be an issue of interest to the media," Modi said.
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"Besides, it will come up only in September," he told the Wall Street Journal, referring to the three-year term of Rajan which ends in September.
"Do you support the reappointment of Mr Rajan, the central bank governor?" the Prime Minister was asked.
As an outspoken RBI Governor, Rajan has expressed his views on host of issues, including intolerance and has even described India as 'one-eyed king' in the land of blind in reference to the country's high economic growth.
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BJP MP Subramanian Swamy has levelled allegations against Rajan including of sending confidential and sensitive financial information around the world and asked the Prime Minister to sack him immediately.
The BJP leader also accused Rajan of publicly disparaging the Modi government and alleged that he is a member of "a US dominated group" that was set up to defend America's dominant position in the global economy.
Finance minister Arun Jaitley has said RBI and the government are in continuous dialogue and that relationship will continue.
Jaitley also said that he does not approve of "personal comments" against anyone including the RBI governor.