June 22, 2010  -- President Obama recalled the top U.S. general in the Afghanistan War, Gen. Stanley McChrystal, following a magazine interview in which McChrystal criticized several top U.S. officials and said he felt betrayed by the U.S. ambassador to Afghanistan.

In a profile by Michael Hastings, published in Rolling Stone, titled "The Runaway General," McChrystal is characterized as an outsider who did not relate well with the administration, and as a military leader who was "disappointed" with his first meeting with the president.

The subhead of the story reads: "Stanley McChrystal, Obama's top commander in Afghanistan, has seized control of the war by never taking his eye off the real enemy: The wimps in the White House."

After news of the comments sent shockwaves through political and military circles from D.C. to Afghanistan, McChrystal quickly issued an apology for his "bad judgment."

"I extend my sincerest apology for this profile. It was a mistake reflecting poor judgment and should never have happened," McChrystal said in a statement. "Throughout my career, I have lived by the principles of personal honor and professional integrity. What is reflected in this article falls far short of that standard."

According to ABC News' senior foreign affairs correspondent Martha Raddatz, who first reported that the general was ordered back to Washington for a monthly staff meeting that he usually attends by videoconference, government officials said it's unlikely he'll lose his job over the comments. Sources tell Raddatz that McChrystal has not mentioned offering his resignation and that the upheaval surrounding the article has yet to sink in.

Duncan Boothby, a civilian press official in Afghanistan, resigned in the aftermath of the scandal, sources tell Raddatz. McChrystal's top press aide Adm. Greg Smith will be traveling with McChrystal back to Washington, D.C.

One of the article's most disparaging remarks comes from an unnamed adviser to McChrystal, who described the general's first meeting with Obama.

"Obama clearly didn't know anything about him, who he was," the aide said. "Here's the guy who's going to run his [expletive] war, but he didn't seem very engaged. The boss was pretty disappointed."

In his apology, McChrystal said he had "enormous respect and admiration for President Obama and his national security team, and for the civilian leaders and troops fighting this war" and said he remains "committed to ensuring its successful outcome."

In the article, McChrystal said the president criticized him for speaking too bluntly about needing more troops last fall.

"I found that time painful," McChrystal said in the article. "I was selling an unsellable position."

McChyrstal also said he felt betrayed by U.S. ambassador to Afghanistan Karl Eikenberry for the ambassador's criticism of Afghan president Hamid Karzai in a leaked cable.

The U.S. embassy in Kabul released a statement, saying: "We have seen the article and General McChrystal has already spoken to it. As Ambassador Eikenberry has said on many occasions, he and General McChrystal are both are fully committed to the President's strategy and to working together as one civilian-military team to implement it."

A U.S. embassy spokesperson said McChrystal called Richard Holbrooke, U.S. special envoy to Pakistan and Afghanistan, "to apologize for this story and accept full responsibility for it."

"Ambassador Holbrooke values his close and productive relationship with General McChrystal and the International Security Assistance Force," the statement read.

Hastings' story details the tense relationship between Holbrooke and McChrystal. On a trip to Paris, when McChrystal saw on his Blackberry that he had received an e-mail from Holbrooke, he groaned: "I don't even want to open it."

"The Boss says he's like a wounded animal," an unnamed member of McChrystal's team is quoted as saying.

NATO Calls Comments 'Unfortunate'

In addition to the written statement, McChrystal has been reportedly calling nearly every figure mentioned in the article to apologize, including NATO allies.

Democratic Sen. John Kerry, D-Mass., chairman of the Senate Foreign Relations committee who was criticized in the article by one of McChrystal's aides, said today he has "tremendous respect" for McChrystal and that it will be up to President Obama to decide whether the general can continue to serve effectively in his position.

"We would all best be served by staying cool and calm," Kerry said today. "This would best be handled by the president and his top general discussing this."

Sen. John McCain, R-Ariz., would not comment on the interview.

An unnamed aide was quoted in the story, saying politicians like McCain and Kerry "turn up, have a meeting with Karzai, criticize him at the airport press conference, then get back for the Sunday talk shows. Frankly, it's not very helpful."

NATO officials were quick with their own response, noting that while "unfortunate," "it is just an article."

"We are in the middle of a very real conflict, and the Secretary General has full confidence in Gen. McChrystal as the NATO commander, and in his strategy," NATO said in a statement.

According to ABC News' Raddatz, the nature of the comments to the magazine has rankled the administration.

"This one is really different. This Rolling Stone article is really different. I think it's why the administration is so angry," Raddatz said on "Good Morning America." "This is personal gossip. This is personal laundry it's not about policy, it's not about troops and we're in the middle of a war."

ABC News' Z. Byron Wolf, Jason Ryan, Ann Compton, Jake Tapper, Nick Schifrin and Marisa Bramwell contributed to this report.