Barack Obama will confront General Stanley McChrystal at the White House tomorrow as he decides whether to sack the commander of US and Nato forces in Afghanistan over disparaging and "contemptuous" remarks about senior administration officials, including the president himself.

The White House said "all options are on the table" after an "angry" Obama summoned McChrystal to Washington to explain quotes in the latest issue of Rolling Stone magazine in which the general and his senior aides accuse the US ambassador to Afghanistan of undermining the war, call the president's national security adviser "a joke" and mock Joe Biden, the vice-president. There is also indirect criticism of the president as "uncomfortable and intimidated" by senior military officials.

Obama said he is considering McChrystal's future. "I think it's clear that the article in which he and his team appeared showed poor judgment. But I also want to make sure I talk to him directly before I make any final decisions," he said.

The president added that his decision would be based on what is best for making a success of the war in Afghanistan and that he would be consulting US allies including David Cameron.

However, the mood appeared to be shifting against McChrystal. Earlier the White House spokesman, Robert Gibbs, declined to give assurances about the general's position. He said US efforts in Afghanistan were bigger than one man and that McChrystal was not indispensable.

The general apologised in person and by phone to some of those criticised and issued a statement admitting "a mistake reflecting poor judgment". "I have enormous respect and admiration for President Obama and his national security team," McChrystal said. But it is not clear whether that will be enough to save McChrystal's job after what is the latest of a series of political blunders.

A leading Democratic member of Congress, Dave Obey, chairman of the House appropriations committee, called for him to be sacked. But the general had the backing of the Afghan president, Hamid Karzai, who said he "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".

In the Rolling Stone article, entitled The Runaway General, McChrystal's aides are quoted as saying that he was less than impressed by Obama from the start. The general is described as believing the president looked "uncomfortable and intimidated" among senior military officers. McChrystal was also "disappointed" that the president "didn't know anything about him" during their early meetings.

The general mocks Biden, with whom he crossed swords over counterterrorism strategy. "Are you asking about Vice-President Biden?" McChrystal said. "Who's that?" A top adviser responds: "Biden? Did you say 'Bite me'?"

But the most stinging criticism is of other senior American officials with responsibility for what is now America's longest war, including the US ambassador to Kabul, Karl Eikenberry, Obama's special representative to Afghanistan, Richard Holbrooke, and the president's national security adviser, Jim Jones.

Rolling Stone quotes McChrystal's aides as calling Jones "a clown" who is "stuck in 1985". Holbrooke is described as being "like a wounded animal".

"Holbrooke keeps hearing rumours that he's going to get fired, so that makes him dangerous," said an aide. The magazine describes how McChrystal at one point checks his BlackBerry. "Oh, not another email from Holbrooke," he said. "I don't even want to open it."

Rolling Stone reports that Eikenberry cannot stand it that his former subordinate is now in charge. Earlier this year, the New York Times published a scathing critique by Eikenberry, a general in Afghanistan for three years early in the war, of McChrystal's military strategy.

It criticised Karzai and warned that the US risked becoming ever more deeply engaged, with no way to extricate itself. McChrystal told Rolling Stone he felt "betrayed" by the leak and questioned Eikenberry's motives: "Here's one that covers his flank for the history books. Now if we fail, they can say 'I told you so'."

The aides also criticise leading politicians, including Senators John McCain and John Kerry, for turning up in Afghanistan, criticising Karzai and then getting back to Washington for the Sunday talk shows.

But the secretary of state, Hillary Clinton, is praised by the general's aides for watching his back and giving him "what he needs".

Rolling Stone said the general was present when many of the comments quoted were made by his aides. The entire tone of the article has infuriated the White House, but the president now faces a dilemma.

Obama became the first president in more than 50 years to sack a top general in wartime when he removed the then US commander in Afghanistan, David McKiernan, and replaced him with McChrystal. To fire McChrystal now would suggest misjudgment by the president as well as removing the architect of an Afghan military strategy that is far from complete. But it may be politically difficult to leave in place a general who has shown such public lack of confidence in those appointed by the White House to work with him.

McChrystal did not make any friends at the White House when his confidential report urging Obama to send 40,000 more troops to Afghanistan leaked.

The administration felt that the general was trying to strongarm the president by making him look weak if he did not agree. Obama did agree to most of McChrystal's request, including another 30,000 troops.

What McChrystal said

It describes how, even though the general voted for Barack Obama, the two failed to connect. McChrystal thought Obama looked "uncomfortable and intimidated" by the roomful of military brass at their first meeting. A second, one-onto-one encounter at the White House did not go much better.

"Obama clearly didn't know anything about him, who he was. Here's the guy who's going to run his fucking war, but he didn't seem very engaged. The boss was pretty disappointed," an aide to McChrystal told the magazine.

Later, McChrystal objected to going to an official Nato dinner in Paris: "I'd rather have my ass kicked by a roomful of people than go out to this dinner." One of the aides was asked by Rolling Stone who the dinner was with. "Some French minister," he replied. "It's fucking gay."

The article describes the behaviour of McChrystal and his aides, who call themselves Team America, at an Irish bar in Parisare were reportedly drunk, while two officers did an Irish jig, mixed with steps from a traditional Afghan wedding dance. They were singing a slurred song about Afghanistan. McChrystal said: "I'd die for them. And they'd die for me."

An unnamed British officer is quoted as saying: "The fucking lads love Stan McChrystal. You'd be out in Somewhere, Iraq, and someone would take a knee beside you and a corporal would be like 'Who the fuck is that?' And it's fucking Stan McChrystal."

The article relates the story of a 25-year-old staff sergeant, Israel Arroyo, who sent an email to McChrystal from the front line in Afghanistan: "I am writing because it was said you don't care about the troops and have made it harder to defend ourselves".

The general replied within hours: "I'm saddened by accusations that I don't care about soldiers, as it is something I suspect any soldier takes both personally and professionally – at least I do. But I know perceptions depend upon your perspective at the time, and I respect that every soldier's view is his own".

McChrystal then turned up at Arroyo's base and went on foot patrol with him in an attempt to understand what the soldier meant.

During a later visit to the same forward base after a soldier is killed, another soldier said to McChrystal: "Sir, some of the guys here, sir, think we're losing, sir."

The general tried to explain his counter-insurgency strategy but afterwards said he did not think it had been been persuasive.

"This is the philosophical part that works with thinktanks. But it doesn't get the same reception from infantry companies," he said.

A senior aide to McChrystal said that the war would be even more unpopular with Americans if they thought about it: "If Americans pulled back and started paying attention to this war, it would become even less popular."