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WASHINGTON — The top U.S. military commander for the Middle East resigned Tuesday amid speculation about a rift over U.S. policy on Iran.

Defense Secretary Robert Gates said that Adm. William Fallon, whose area of responsibility includes Iraq, had asked for permission to retire and that Gates agreed. Gates said the decision, effective March 31, was entirely Fallon’s and that Gates believed it was “the right thing to do.”

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

“Recent press reports suggesting a disconnect between my views and the president’s policy objectives have become a distraction at a critical time and hamper efforts in the Centcom region,” Fallon, who is traveling in Iraq, said in a statement issued by his U.S. headquarters in Tampa, Fla.

“And although I don’t believe there have ever been any differences about the objectives of our policy in the Central Command area of responsibility, the simple perception that there is makes it difficult for me to effectively serve America’s interests there,” he said.

President Bush praised Fallon in a statement. “During his tenure at Centcom, Adm. Fallon’s job has been to help ensure that America’s military forces are ready to meet the threats of an often-troubled region of the world, and he deserves considerable credit for progress that has been made there, especially in Iraq and Afghanistan,” Bush said.

Gates announced that Fallon’s top deputy, Army Lt. Gen. Martin Dempsey, would take over temporarily when Fallon leaves. A permanent successor, requiring nomination by the president and confirmation by the Senate, might not be designated in the near term.

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

“I don’t think there were differences at all,” Gates said, adding that he believed Fallon was fully supportive of the administration’s policy on dealing with Iran through diplomatic and economic pressures.

Fallon, 63, a veteran of the Vietnam War and a former vice chief of naval operations, has had a 41-year Navy career. He took the Central Command post on March 16, 2007, succeeding Army Gen. John Abizaid, who retired.

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