March 11, 2008  -- Adm. William Fallon, the top U.S. military commander for the Middle East, has resigned, citing a magazine article which suggested he was at odds with President Bush's policy toward Iran.

In a statement released by U.S. Central Command, Fallon disputed a recent Esquire magazine article that suggested differences between his views and administration policies concerning Iran.

"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 said in a written statement released from his Tampa, Fla., office.

"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," Fallon's statement read.

"I have, therefore, concluded that it would be best to step aside and allow the secretary and our military leaders to move beyond this distraction ... and focus on the achievement of our strategic objectives in the region. I have submitted my request to retire to the secretary of defense."

Magazine: Fallon Standing Between Bush and Iran

In the Esquire interview , Fallon is described as the only man standing between the Bush administration and war with Iran.

"If, in the dying light of the Bush administration, we go to war with Iran, it'll all come down to one man. If we do not go to war with Iran, it'll come down to the same man. He is that rarest of creatures in the Bush universe: the good cop on Iran, and a man of strategic brilliance. His name is William Fallon," reads the magazine article.

In announcing Fallon's resignation Tuesday, Defense Secretary Robert Gates said it was "a cumulative kind of thing. It isn't the result of any one article or any one issue."

When asked if today's announcement might be interpreted as a move closer toward military action against Iran, Gates said, "that's ridiculous, just ridiculous. ... The notion that this portends anything in change of Iran policy is, to quote myself, ridiculous."

Gates said Tuesday that Fallon had asked him for permission to retire and Gates agreed. Gates said it was "the right thing to do."

Administration Rhetoric 'Not Helpful'

Gates also said there was a "misperception" that Fallon disagreed with the administration's approach to Iran.

In the article, Fallon is quoted as saying Bush administration rhetoric against Iran is "not helpful."

The article reads: "So while Adm. Fallon's boss, President George W. Bush, regularly trash-talks his way to World War III and his administration casually casts Iranian President Mahmoud Ahmadinejad as this century's Hitler (a crown it has awarded once before, to deadly effect), it's left to Fallon — and apparently Fallon alone — to argue that.

"As he told Al Jazeera last fall, 'This constant drumbeat of conflict … is not helpful and not useful. I expect that there will be no war, and that is what we ought to be working for. We ought to try to do our utmost to create different conditions,'" said the magazine article.

The president Tuesday issued a written statement wishing Fallon and his family the best.

"During his tenure at Centcom, 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 wrote.

Fallon is in Baghdad, making the rounds to speak to all of his commanders.

ABC News' Martha Raddatz spoke to Fallon Tuesday as he waited to go in and see Gen. David Petraeus, the U.S. commander in Iraq.

Fallon told ABC News that he sensed the Esquire article angered members of the Bush administration.

A senior administration official met with Gates as soon as the article came out and was very worried about the reaction from the White House at that time.

Fallon told Raddatz he is grateful for the way Gates handled his resignation.

Democrats on Capitol Hill seized on the resignation as more evidence that the Bush administration "silences opposing voices."

"Yet another example that independence and the frank, open airing of experts' views are not welcomed in this administration," read a statement from Senate Majority Leader Harry Reid.

"It is also a sign that the administration is blind to the growing costs and consequences of the Iraq War, which has so damaged America's security interests in the Middle East and beyond," Reid said.

Fallon, who has had a 41-year career in the Navy, took the central command post March 16, 2007, succeeding Army Gen. John Abizaid, who retired. Fallon previously served as commander of U.S. Pacific Command.

His resignation was applauded by Adm. Michael Mullen, chairman of the Joint Chiefs of Staff.

"I support Secretary Gates' decision to accept Adm. Fallon's letter of resignation and request for retirement. I also respect the reasons for which Adm. Fallon submitted it and applaud his ability to recognize the responsibility before him," Mullen said in a written statement.

"He had an enormous impact not only on the way we operate and fight in this new century, but also on the way in which we stay engaged globally," Mullen's statement read.

Gates said that until a permanent replacement is nominated and confirmed by the Senate, Fallon's place will be taken by his top deputy, Army Lt. Gen. Martin Dempsey.

ABC News' Zach Wolf, Ann Compton, John Cochran and Jennifer Duck contributed reporting.