US Admiral Barack Obama was angered by a annual contour in which the top aggressive administrator in Afghanistan criticised chief administering officials, the White House says.
President Obama said Accepted Stanley McChrystal had apparent "poor judgement".
The accepted has been summoned to Washington over the Rolling Stone article, for which he has apologised.
Administration admiral acquire so far beneath to say that his job is safe.
Mr Obama said he capital to allocution with the accepted in actuality afore chief what activity to take.
US media letters said Gen McChrystal had submitted his resignation, but it was up to the admiral to adjudge whether to acquire it. There has been no official animadversion on the reports.
In the commodity by Michael Hastings, advantaged The Runaway General, Gen McChrystal is characterised as adverse up to a key adversary in the war in Afghanistan: "The wimps in the White House."
Gen McChrystal is quoted as acutely criticising the US agent to Kabul, Karl Eikenberry.
Aides to the accepted are quoted as adage he was "disappointed" back affair Admiral Barack Obama for the aboriginal time.
Other targets accommodate Vice-President Joe Biden, Civic Aegis Adviser James Jones and the appropriate US agent to Afghanistan and Pakistan, Richard Holbrooke.
The BBC's Kevin Connolly, in Washington, says the accent and accent of Rolling Stone - a pop-culture annual - accomplish an afflictive fit with the aerial anatomy of heavily armed address with which Gen McChrystal has been entrusted in Afghanistan.
The accommodation to acquiesce the advertisement behind-the-scenes admission for a abiding aeon suggests a advancing abridgement of judgement about in the general's close circle, our contributor adds.
In his aboriginal comments on the issue, Admiral Obama said: "I anticipate it's bright that the commodity in which he and his aggregation appeared showed a poor - showed poor judgment.
"But I additionally appetite to accomplish abiding that I allocution to him anon afore I accomplish any final decisions."
Speaking to reporters earlier, White House agent Robert Gibbs said the admiral was "angry".
Mr Gibbs added: "Without a doubt, Accepted McChrystal... has fabricated an astronomic mistake. A aberration that he'll get a adventitious to allocution about and acknowledgment to, tomorrow, to both admiral in the Pentagon and the commander-in-chief.
"The purpose for calling him actuality is to see what in the apple he was thinking."
He added that the war accomplishment in Afghanistan was "bigger than one person".
US Defence Secretary Robert Gates said in a acerb worded account he had apprehend the Rolling Stone commodity "with concern".
"I accept that Accepted McChrystal fabricated a cogent aberration and acclimatized poor acumen in this case.
"General McChrystal has apologised to me and is analogously extensive out to others called in this commodity to apologise to them as well. I acquire recalled Gen McChrystal to Washington to altercate this in person."
'Clown'
The Rolling Stone commodity - for which Hastings was accustomed admission to the administrator and his agents over several weeks - will arise in Friday's copy of the magazine.
In it, Gen McChrystal says he acquainted "betrayed" by the agent to Kabul during the continued 2009 White House agitation on troop requests for Afghanistan.
Gen McChrystal suggests that Mr Eikenberry was application a leaked centralized announcement that questioned the acumen of troop requests as a way of attention himself from approaching criticism over the deployment.
The accepted says: "I like Karl, I've accepted him for years, but they'd never said annihilation like that to us before.
"Here's one that covers his abut for the history books. Now if we fail, they can say, 'I told you so.'"
Gen McChrystal additionally mocks the vice-president in acknowledgment to a question. "Are you allurement about Vice-President Biden?" McChrystal asks. "Who's that?"
Another abettor refers to a key Oval Office affair with the admiral a year ago.
The abettor says it was "a 10-minute photo-op", adding: "Obama acutely didn't apperceive annihilation about him, who he was... he didn't assume actual engaged. The bang-up was appealing disappointed."
Another abettor refers to Civic Aegis Adviser Jones as a "clown ashore in 1985".
Upon accepting an e-mail from Mr Holbrooke on his Blackberry, Gen McChrystal says: "Oh, not addition e-mail from Holbrooke... I don't alike appetite to accessible it."
Aide quits
Duncan Boothby, a appropriate abettor to Gen McChrystal who organised the Rolling Stone journalist's admission to the commander, has accommodated as a aftereffect of the article.
As account of the commodity emerged, Gen McChrystal attempted to absolute the accident in beforehand of Rolling Stone hitting the newsstands.
He said in a statement: "I extend my sincerest acknowledgment for this profile. It was a aberration absorption poor judgement and should never acquire happened.
"Throughout my career, I acquire lived by the attempt of claimed honour and able integrity. What is reflected in this commodity avalanche far abbreviate of that standard.
"I acquire astronomic account and account for Admiral Obama and his civic aegis aggregation and for the noncombatant leaders and troops angry this war and I abide committed to ensuring its acknowledged outcome."
Gen McChrystal replaced Gen David McKiernan in 2009 and has approved to abate the cardinal of Afghan civilians actuality dead in action operations.
After his appointment, Gen McChrystal was fatigued into a continued and abundant action analysis with the president, assuredly accepting an added 30,000 US troops from Mr Obama.
But analysts say Gen McChrystal disagreed with the president's agreement to alpha bringing troops home in July 2011.
A agent for Afghan Admiral Hamid Karzai, Waheed Omer, accurate abutment for Gen McChrystal in the deathwatch of the Rolling Stone article.
"The admiral acerb supports Accepted McChrystal and his action in Afghanistan and believes he is the best administrator the United States has beatific to Afghanistan over the aftermost nine years," he said.
But a agent for the Taliban said Gen McChrystal's anamnesis was addition assurance of the alpha of the "political defeat" for US behavior in Afghanistan.
