Mr Gates said the Joint Forces Command would close, the use of outside contractors would be cut and the number of generals and admirals reduced.
He has said that he wants to find savings of about US$100 billion in the military budget in the next five years. Mr Gates said he wanted to free up spending for frontline requirements.
In a Pentagon news conference, he said the military had grown unwieldy and costly following the terrorist attacks of 11 September 2001.
The Joint Forces Command, based in Virginia, employs 5,000 people and trains troops from the different services to work together.
Calling the US military "top-heavy", Mr Gates, who was appointed by George W Bush in 2006, said he would recommend eliminating at least 50 positions for generals and admirals.
And he recommended cutting the number of support contractors by 10 percent.
The US Department of Defense will spend more than US$700bn this year, more than any other military service in the world.
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