A team that included European aerospace giant EADS won the 35-billion-dollar contract to supply refuelling aircraft on February 29, setting off a storm of protests among supporters of US rival Boeing in the US Congress.
Some Democrats blamed the loss of the contract on McCain, the presumptive Republican presidential nominee, because he fought an earlier air force deal to lease tanker planes from Boeing.
That deal collapsed amid an influence peddling scandal that ousted the company's CEO and sent two executives to prison.
McCain has avoided commenting on the tanker contract.
But the Pentagon on Tuesday released a letter that Gates sent to McCain on January 26, 2007, just days before the air force issued a request for proposals for the contract to build new tanker planes.
In it, Gates alludes to changes made in a draft of the request for proposal, but does not say what they were or specify what concerns McCain had raised.
"You have expressed to me on several occasions your concerns with the Air Force's Tanker Replacement Program," the letter said.
"A quick check tells me that the Air Force has already modified the draft RFP (request for proposal) in response to a number of concerns.
"I understand that these modifications have now been shared with industry and briefed to your staff and that they are responsive to the concerns identified in your letter."
Gates thanked McCain for raising his concerns and said he agreed that "the competition for this important program must be conducted in a full, open and transparent manner."