The US military agency is "working through appropriate channels...To acquire a limited amount of leased space in Trump Tower," Lt Col J B Brindle, a Pentagon spokesman, told The Washington Post in a statement.
"The space is necessary for the personnel and equipment who will support the POTUS at his residence in the building," Brindle said.
The space will be separate from the Secret Service detail that is routinely based in Trump's signature midtown tower, where his private company, the Trump Organisation, is headquartered and where he owns a lavish triplex penthouse.
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, the report said.
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"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 1980s and still owns it," it said.
The military interest in Trump Tower could reinvigorate questions over how much Trump properties are benefiting from his public office, the report said.
Trump has resisted calls to divest his financial stake in business interests, although he has resigned from his official management roles and left the companies' operations to his adult sons and a longtime executive in his company.