Obama press secretary Robert Gibbs said "the magnitude and greatness of the mistake here are profound" and repeatedly declined to say McChrystal's job was safe. "All options are on the table," he said.
Defense Secretary Robert Gates said the commander's comments were "distractions" to the war in Afghanistan.
McChrystal publicly apologized Tuesday for using "poor judgment" in interviews for a story in Rolling Stone. He then left Afghanistan to appear, as ordered by Obama, at the White House on Wednesday.
He'll be expected to explain his comments to the president and Pentagon officials who, as Gibbs put it, want "to see what in the world he was thinking." The presidential spokesman said Obama acknowledged McChrystal's apology and believed he deserved a chance to explain himself.
However, military leaders rarely challenge their commander in chief publicly and when they do, consequences tend to go beyond a scolding. And Gibbs left little doubt that a firing was probably in the offing. "Our efforts in Afghanistan are bigger than one person," he told reporters several times.
A decision on McChrystal's future will be announced by the White House after Wednesday's meeting, Gibbs said.
A top military official in Afghanistan told The Associated Press that McChrystal hasn't been told whether he will be allowed to keep his job. The official spoke on condition of anonymity to describe internal discussions between Washington and the general's office in Kabul. Gibbs said McChrystal had not offered his resignation, in part because he has not yet spoken to or seen Obama, who was angry when his press secretary gave him the story Monday night.
Gibbs refused to describe how angry the president was, except to say: "You would know it if you saw it."
McChrystal spent Tuesday calling several others mentioned in the article to apologize, officials said, including Gates and Richard Holbrooke, U.S. special envoy to Pakistan.
Gates issued a statement saying McChrystal made "a significant mistake" and used poor judgment in his remarks to a magazine reporter.
"We are fighting a war against al-Qaida and its extremist allies, who directly threaten the United States, Afghanistan, and our friends and allies around the world," Gates said. "Going forward, we must pursue this mission with a unity of purpose. Our troops and coalition partners are making extraordinary sacrifices on behalf of our security, and our singular focus must be on supporting them and succeeding in Afghanistan without such distractions."
Holbrooke's office said in a terse two-line statement that McChrystal had called him in Kabul "to apologize for this story and accept full responsibility for it." It said Holbrooke "values his close and productive relationship with General McChrystal."
A spokesman said Chairman of the Joint Chiefs of Staff Adm. Mike Mullen told McChrystal of his "deep disappointment" over the article.
But in Kabul, President Hamid Karzai issued a statement calling McChrystal the "best commander" of the war. Karzai spokesman Waheed Omar said Karzai hopes that Obama doesn't decide to replace him.
In the article, McChrystal complains that Obama handed him "an unsellable position" on the war, back when the commander was pressing for more troops than the administration was then prepared to send. "I found that time painful," he said.
McChrystal also said he was "betrayed" by Ambassador Karl Eikenberry, the man the White House chose to be his diplomatic partner in Afghanistan. He accused Eikenberry of raising doubts about the reliability of Afghan President Hamid Karzai only to give himself cover in case the U.S. effort failed.
"Here's one that covers his flank for the history books," McChrystal told the magazine. "Now, if we fail, they can say 'I told you so."'
Obama appointed McChrystal to lead the Afghan war in May 2009.
In Kabul on Tuesday, McChrystal issued a statement saying: "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."
"I extend my sincerest apology for this profile," the statement said. "It was a mistake reflecting poor judgment and should never have happened."v Mullen talked with McChrystal about the article Monday night, Capt. John Kirby, Mullen's spokesman said. In a 10-minute conversation, the chairman "expressed his deep disappointment in the piece and the comments" in it, Kirby said.
The Wednesday meeting at the White House was one of Obama's regular sessions on the Afghanistan war, which McChrystal and others in Afghanistan usually attend via videoconference. Secretary of State Hillary Rodham Clinton and Gates are among those who regularly attend the Situation Room meetings in person.
Sen. John Kerry, D-Mass., chairman of Senate Foreign Relations Committee, called for all involved to "stay cool and calm" and not the let situation interfere with the mission in Afghanistan.
He said he had "enormous respect" for the general and had spoken to McChrystal on Tuesday morning and "emphasized to him that I think, obviously, those are comments that he is going to have to deal with with respect to the commander in chief, the vice president and his national security staff."