US President Barack Obama was angered by a magazine profile in which the top military commander in Afghanistan criticised senior administration officials, the White House says.
President Obama said General Stanley McChrystal had shown "poor judgement".
The general has been summoned to Washington over the Rolling Stone article, for which he has apologised.
Administration officials have so far declined to say that his job is safe.
Mr Obama said he wanted to talk with the general in person before deciding what action to take.
US media reports said Gen McChrystal had submitted his resignation, but it was up to the president to decide whether to accept it. There has been no official comment on the reports.
In the article by Michael Hastings, entitled The Runaway General, Gen McChrystal is characterised as facing up to a key enemy in the war in Afghanistan: "The wimps in the White House."
Gen McChrystal is quoted as sharply criticising the US ambassador to Kabul, Karl Eikenberry.
Aides to the general are quoted as saying he was "disappointed" when meeting President Barack Obama for the first time.
Other targets include Vice-President Joe Biden, National Security Adviser James Jones and the special US envoy to Afghanistan and Pakistan, Richard Holbrooke.
The BBC's Kevin Connolly, in Washington, says the language and tone of Rolling Stone - a pop-culture magazine - make an uncomfortable fit with the delicate form of heavily armed diplomacy with which Gen McChrystal has been entrusted in Afghanistan.
The decision to allow the publication behind-the-scenes access for a prolonged period suggests a disturbing lack of judgement somewhere in the general's inner circle, our correspondent adds.
In his first comments on the issue, President Obama said: "I think it's clear that the article in which he and his team appeared showed a poor - showed poor judgment.
"But I also want to make sure that I talk to him directly before I make any final decisions."
Speaking to reporters earlier, White House spokesman Robert Gibbs said the president was "angry".
Mr Gibbs added: "Without a doubt, General McChrystal... has made an enormous mistake. A mistake that he'll get a chance to talk about and answer to, tomorrow, to both officials in the Pentagon and the commander-in-chief.
"The purpose for calling him here is to see what in the world he was thinking."
He added that the war effort in Afghanistan was "bigger than one person".
US Defence Secretary Robert Gates said in a strongly worded statement he had read the Rolling Stone article "with concern".
"I believe that General McChrystal made a significant mistake and exercised poor judgment in this case.
"General McChrystal has apologised to me and is similarly reaching out to others named in this article to apologise to them as well. I have recalled Gen McChrystal to Washington to discuss this in person."
The Rolling Stone article - for which Hastings was given access to the commander and his staff over several weeks - will appear in Friday's edition of the magazine.
In it, Gen McChrystal says he felt "betrayed" by the ambassador to Kabul during the long 2009 White House debate on troop requests for Afghanistan.
Gen McChrystal suggests that Mr Eikenberry was using a leaked internal memo that questioned the wisdom of troop requests as a way of protecting himself from future criticism over the deployment.
The general says: "I like Karl, I've known him for years, but they'd never said anything like that to us before.
"Here's one that covers his flank for the history books. Now if we fail, they can say, 'I told you so.'"
Gen McChrystal also mocks the vice-president in response to a question. "Are you asking about Vice-President Biden?" Gen McChrystal asks. "Who's that?"
Another aide refers to a key Oval Office meeting with the president a year ago.
The aide says it was "a 10-minute photo-op", adding: "Obama clearly didn't know anything about him, who he was... he didn't seem very engaged. The boss was pretty disappointed."
Another aide refers to National Security Adviser Jones as a "clown stuck in 1985".
Upon receiving an e-mail from Mr Holbrooke on his Blackberry, Gen McChrystal says: "Oh, not another e-mail from Holbrooke... I don't even want to open it."
Duncan Boothby, a special assistant to Gen McChrystal who organised the Rolling Stone journalist's access to the commander, has resigned as a result of the article.
As news of the article emerged, Gen McChrystal attempted to limit the damage in advance of Rolling Stone hitting the newsstands.
He said in a statement: "I extend my sincerest apology for this profile. It was a mistake reflecting poor judgement and should never have happened.
"Throughout my career, I have lived by the principles of personal honour and professional integrity. What is reflected in this article falls far short of that standard.
"I have enormous respect and admiration for President Obama and his national security team and for the civilian leaders and troops fighting this war and I remain committed to ensuring its successful outcome."
Gen McChrystal replaced Gen David McKiernan in 2009 and has sought to reduce the number of Afghan civilians being killed in combat operations.
After his appointment, Gen McChrystal was drawn into a long and detailed strategy review with the president, finally getting an additional 30,000 US troops from Mr Obama.
But analysts say Gen McChrystal disagreed with the president's pledge to start bringing troops home in July 2011.
A spokesman for Afghan President Hamid Karzai, Waheed Omer, voiced support for Gen McChrystal in the wake of the Rolling Stone article.
"The president strongly supports General McChrystal and his strategy in Afghanistan and believes he is the best commander the United States has sent to Afghanistan over the last nine years," he said.
But a spokesman for the Taliban said Gen McChrystal's recall was another sign of the start of the "political defeat" for US policies in Afghanistan.