Updated

Navy Adm. William Fallon, the head of U.S. Central Command, which leads U.S. operations in Iraq and Afghanistan, is stepping down, Defense Secretary Robert Gates announced Tuesday.

Fallon claimed ongoing misperceptions about differences between his ideas and U.S. policy are making it too difficult for him to operate, Gates said, agreeing. He added that the differences are not extreme, but the misperception had become too great.

"I believe it was the right thing to do, even though I do not believe there are, in fact, significant differences between his views and administration policy," Gates said at a Pentagon news conference, noting that he accepted the request to retire with "reluctance and regret."

"I don't know whether he was misinterpreted or whether people attributed views to him that were not his views, but clearly there was a concern," Gates said.

The misperceptions relate to an article published last week in Esquire magazine that portrayed Fallon 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.

In a statement distributed by Centcom headquarters in Tampa, Fla., Fallon said he requested permission to step down because the article showed disrespect toward the president and caused embarrassment and distractions that were the result of misrepresentations of his views of Centcom missions.

"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. 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 said.

"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," he continued.

In a statement issued by the White House, Bush said Fallon "has served his country with honor, determination and commitment."

"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.

Democrats jumped on the news, expressing concern over the admiral's departure.

"Admiral Fallon's decision to resign is a disappointment to those of us who viewed his reputation for candor as an essential asset in his role as Centcom commander," said House Speaker Nancy Pelosi. "Although his views on the best way to deal with the challenges in Centcom's area of responsibility may not have matched those held by White House officials, Adm. Fallon was viewed in Congress as someone who was careful, forthright and direct."

"I can only hope that the decision to retire was his own," said Senate Armed Services Committee Chairman Carl Levin, D-Mich.

House Armed Services Committee Chairman Ike Skelton, D-Mo., asked Fallon on Tuesday to appear jointly at an upcoming April Iraq progress hearing with Petraeus and Amb. Ryan Crocker, FOX News learned. The chairman was told the admiral would have to get back with him, but hours later, Fallon resigned.

Gates said it is "ridiculous" to assume that because Fallon is leaving, the U.S. is preparing war against Iran or has changed its policy at all toward Iran.

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

It was often reported that he and Gen. David Petraeus butted heads about troop levels in Iraq, which the two denied, but was an ongoing dispute that simmered below the surface within the Pentagon. Fallon is responsible for not only Iraq and Afghanistan. The article noted that the troop numbers were so taxed in Iraq that it was hurting operations in Afghanistan.

Gates said he didn't think it was one event that led to Fallon's request for removal from his post.

"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."

Fallon has had a 42-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. He served in Vietnam and commanded an air wing in Desert Storm.

"Fox Fallon has dedicated his life to the preservation of the freedoms we in this nation enjoy today, and all Americans should be deeply grateful for his dedication," Gates said, noting that his departure will create a hole in the strategic planning conducted by Centcom.

Centcom's second-in-command Lt. Gen. Martin Dempsey will now take over Fallon's post, effective March 31.

FOX News' Jennifer Griffin, Bret Baier and The Associated Press contributed to this report.