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

Defense Secretary Robert Gates said that Adm. William J. 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, who previously was commander of U.S. Pacific Command, 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 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.

U.S. Sen. Daniel K. Akaka, D-Hawai'i, said in a statement that Fallon's resignation represents a "significant loss to our military and our nation at a time when our armed forces need a strong, independent leader who is willing to make honest assessments of this administration's strategic policies."

"Adm. Fallon's decision to resign is yet one more example of this administration silencing our top military leaders," Akaka said. "It is not only necessary but mandatory that these military experts who have spent years in the field serving our country have the ability to express their concerns without fear of censure or reprisal."

U.S. Sen. Daniel K. Inouye, D-Hawai'i, chairman of the Senate Appropriations defense subcommittee, said he was sorry Fallon's "brilliant career come to an end this way."

"His service to our nation has been invaluable, and we owe him much," Inouye said.

U.S. Rep. Neil Abercrombie, D-Hawai'i, declined to comment on Fallon's resignation until he knew more about it, said Dave Helfert, spokesman for the congressman.

U.S. Rep. Mazie Hirono, D-Hawai'i, said she met Fallon during his time as commander of the U.S. Pacific Command, a post he held before appointed last year as head of Central Command.

"I would like to thank Admiral Fallon for serving the people of Hawai'i, and our country, with distinction and honor," she said.

President Bush praised Fallon in a statement. "During his tenure at Centcom, Admiral 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, will 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.

Dempsey could be elevated to Central Command chief, although he already has been selected to become the top U.S. Army general in Europe. Among other possible candidates for the post — considered one of the most important in the U.S. military — is Army Lt. Gen. Stanley McChrystal, who had just been named to a top post on the Joint Chiefs of Staff and who had been commander of U.S. special operations forces in Iraq.

Another possibility is Army Lt. Gen. Peter Chiarelli, who serves as Gates' senior military assistant and is a former senior commander in Iraq.

Gates described as "ridiculous" any notion that Fallon's departure signals the United States 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 added. He said 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. Fallon previously served as commander of U.S. Pacific Command.

Gates called 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," said Gates, speaking of the circumstances leading up to Fallon's decision. "It isn't the result of any one article or any one issue."

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Advertiser Washington Bureau Dennis Camire and Lolita C. Baldor of The Associated Press contributed to this story.