Defence officials made similar arrangements for past presidents, including at the Chicago home of Barack Obama, to offer support for day-to-day operations of the president and his staff.
But the prospect of a government agency paying rent to a company owned by the president again raises additional questions about the mingling of Trump's financial interests with his presidency.
Trump led the development of the Fifth Avenue skyscraper in the '80s, and still owns it today.
Defence officials would not say what they expected to spend on the space. But CNN, which first reported the news, quoted a leasing agent who estimated renting a floor in Trump Tower can cost about US$1.5 million ($2 million) a year.
Trump Organisation and White House officials did not respond to requests for comment.
The military interest in Trump Tower could reinvigorate questions over how much Trump properties are benefiting from Trump's public office.
Trump has resisted calls to divest his financial stake in business interests, though he has resigned his official management roles and left the companies' operations to his sons and a long-time Trump executive.
"I have never heard of a president charging rent to the DOD or any other part of the government so they can be near him on his travels," said Richard Painter, a former chief White House ethics counsel under George W. Bush who is part of a lawsuit accusing Trump of violating a constitutional ban for his continued ownership interest in a Washington hotel.
"He should give them for free a very limited amount of space and they can rent nearby if needed."
