Gates asked the president-elect to allow him to keep the staff until replacements are found in order to ensure continuity as military operations in Iraq and Afghanistan continue to percolate through the presidential transition process.
Gates spokesman Geoff Morrell told FOX News on Tuesday that the request -- and the fact that Obama agreed to allow most of the Pentagon appointees to remain -- is "unprecedented."
The request was first reported by The Washington Times. The Times wrote that Gates was trying to prevent a leadership vacuum while U.S. troops are engaged abroad.
The Times reported that Gates' request ensures that key policy positions will not be left to "acting" subordinates during the transition process.
Typically, political appointees would have left their desks by Inauguration Day, Jan. 20.
The Defense Department is the only agency considering such a request. All other political appointees in other branches had to submit their resignation letters by Friday.
"I have received authorization from the president-elect's transition team to extend a number of Department of Defense political appointees an invitation to voluntarily remain in their current positions until replaced," Gates wrote in a letter to appointees on Monday. "This option will be available to all willing political appointees with the exception of those who are contacted individually and told otherwise."
About 100 of the 250 appointees have not been asked to stay on during the transition.
FOX News' Jennifer Griffin contributed to this report.