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Adm. William J. Fallon, one of the most experienced officers in the U.S. military, said the reports were wrong but had become a distraction hampering his efforts in the Middle East. Fallon’s area of responsibility includes Iran and stretches from Central Asia across the Middle East to the Horn of Africa.

“I don’t believe there have ever been any differences about the objectives of our policy in the Central Command area of responsibility,” Fallon said, and he regretted “the simple perception that there is.” He was in Iraq when he made the statement.

Defense Secretary Robert Gates told a Pentagon news conference that he accepted Fallon’s request to resign and retire from the Navy, agreeing that the Iran issue had become a distraction. But Gates said repeatedly that he believed talk of Fallon opposing Bush on Iran was mistaken.

“I don’t think that there really were differences at all,” Gates said, adding that Fallon was not pressured to leave.

“He told me that, quote, ‘The current embarrassing situation, public perception of differences between my views and administration policy, and the distraction this causes from the mission make this the right thing to do,’ unquote,” Gates told reporters.

Fallon was the subject of an article published last week in Esquire magazine that portrayed him as at odds with a president eager to go to war with Iran. Titled “The Man Between War and Peace,” it described Fallon as a lone voice against taking military action to stop the Iranian nuclear program.

Gates said he did not think it was that article alone that prompted Fallon to quit. Rather, Gates thought it was “a cumulative kind of thing” that he and Fallon had failed to put “behind us.”

It is highly unusual for a senior commander to resign in wartime. Fallon took the post on March 16, 2007, succeeding Army Gen. John Abizaid, who retired after nearly four years in the job. Fallon was part of a new team of senior officials, including Gates, chosen by Bush to implement a revised Iraq war policy.

Fallon’s departure, effective March 31, is unlikely to have an immediate effect on conducting the wars in Iraq or Afghanistan. His top deputy at Central Command, Army Lt. Gen. Martin Dempsey, will take his place until a permanent successor is nominated by the president and confirmed by the Senate.

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Pentagon press secretary Geoff Morrell said the White House played no role in Fallon’s move.

“People should not misconstrue this as the price to be paid for speaking out within the Pentagon,” Morrell said. “This is not indicative of a hostile environment toward free thinking. This is indicative of what sadly became a perception problem that dogged Admiral Fallon — this perception that he was in a different place than the president and the administration when it came to Iran.”

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.