WASHINGTON — The top American military commander for the Middle East, Admiral William Fallon, is resigning, Defense Secretary Gates said today.

Mr. Gates said Admiral Fallon had asked him this morning for permission to retire and Mr. Gates agreed. Mr. Gates said the decision was entirely Admiral Fallon’s and that Mr. Gates believed it was “the right thing to do.”

Admiral Fallon was the subject of an article published last week in Esquire magazine that portrayed him as opposed to President Bush’s Iran policy. It described Admiral Fallon as a lone voice against taking military action to stop the Iranian nuclear program.

Mr. Gates described as “ridiculous” any notion that Admiral Fallon’s departure signals America is planning to go to war with Iran. And he said “there is a misperception” that Admiral Fallon disagrees with the administration’s approach to Iran.

“I don’t think there were differences at all,” Mr. Gates said.

Admiral Fallon has had a 41-year Navy career. He took the Central Command post on March 16, 2007, succeeding Army General John Abizaid, who retired. Admiral Fallon previously served as commander of U.S. Pacific Command.

Mr. Gates said that until a permanent replacement is nominated and confirmed by the Senate, Admiral Fallon’s place will be taken by his top deputy, Army Lieutenant General Martin Dempsey.

The secretary called Admiral Fallon a very able military strategist and said his advice will be missed at the Pentagon.

“I think this is a cumulative kind of thing,” Mr. Gates said, speaking of the circumstances leading up to Admiral Fallon’s decision. “It isn’t the result of any one article or any one issue.”

“As I say, the notion that this decision portends anything in terms of change in Iran policy is, to quote myself, ‘ridiculous,’ ” he said.