Defense Secretary Robert Gates backed keeping Gen. Stanley McChrystal on the job because he was vital to the war effort in Afghanistan, but he was overruled, a senior Pentagon official told CNN's Barbara Starr.
The official has direct knowledge of the events but declined to be identified because of the internal administration discussions.
President Barack Obama relieved McChrystal of command of the Afghan war on Wednesday, a day after Rolling Stone published critical comments about top White House officials by members of McChrystal's staff.
Gates was initially furious about the article, but said McChrystal had to stay in command because the war is at such a critical point, a second source - who also asked not to be named on internal administration discussions - told CNN.
But as it became clear the White House didn't feel same way and the issue was not going to fade, Gates shifted his position and agreed that keeping the general would be an untenable distraction.
Technically, McChrystal resigned.
It's still unclear whether Obama had made up his mind before sitting down with McChrystal, but CNN has learned that during their one-on-one meeting, Obama gave the general a chance to defend himself.
"The president asked him about the (Rolling Stone) article," said a senior administration official.
McChrystal "tried to explain the situation," the official said.
That senior administration official, who briefed reporters, said that once Obama accepted McChrystal's resignation, he wasted no time finding his replacement.
After McChrystal walked out of the White House following his 30-minute face-to-face meeting with the president, the president immediately huddled with a team of advisors to decide who would replace McChrystal.
That group included Vice President Joe Biden, Defense Secretary Gates, Joint Chiefs Chairman Adm. Mike Mullen, National Security Advisor Jim Jones and Chief of Staff Rahm Emanuel.
For 45 minutes, they mulled over the president's options.
The White House earlier had asked for a list of possible replacements for McChrystal in the event the president replaced him.
Gen. David Petraeus, head of U.S. Central Command, was one of those considered. The president chose Petraeus.
There is a continuity - Petraeus is familiar with all the players in the region and he is familiar to NATO partners.
Then Obama called Petraeus, who was already in the White House Situation Room, into the Oval Office to ask him to take over the mission in Afghanistan.
The meeting lasted for 40 minutes, and Petraeus agreed.
The senior administration official said despite the fact that Petraeus was asked to give up Central Command, he did not consider it a demotion.
Obama acknowledged the move was not "the normal course" for a top general to go from being in charge of Central Command to taking command in Afghanistan.
The president also acknowledged it was "a sacrifice for Petraeus."
Obama then went to the Situation Room, where his national security team was waiting.
The senior administration official described the president as "stern" as he walked the team through his decision.
The official said the president told everyone, "We need to remember why we're doing this."
Obama went on to explain that it was understandable to have disagreements or tension within his security team, but when those disagreements turn petty, that does not serve the men and women fighting for the mission.
The president expressed "regret" and "sorrow", saying that "this was a sad day", the senior administration official said.
Then Obama wrapped up the meeting, and called Afghanistan's President Hamid Karzai to explain his decision.
McChrystal and Karzai had been close, according to administration and Pentagon officials.
The president then went to the Rose Garden to face the cameras and announce his decision to the American people.
Since then, according to White House spokesman Tommy Vietor, Obama has talked to British Prime Minister David Cameron, House Speaker Nancy Pelosi, and Sens. Harry Reid, Carl Levin and John McCain.
He is urging the Senate to follow his lead and to quickly confirm his nominee.
- CNN White House Correspondents Suzanne Malveaux and Dan Lothian contributed to this report.
If Gates was the President, then perhaps his opinion would truly be substantial or even needed. Since he is not.... back your President!
What ever happened to freedom of speech.
He deserved the firing but funny oblama put in petraus who was bush's lackey. Oblama used to rip him apart.
He still has his free speech and always did....he just lost his job but no one censored him
This is pretty much another sign of the disdain they have for our President due to an obvious and crucial change in the traditional choice for office.The disrespect should never be tolerated and he should be removed immediately.If a President can't trust everyone in his camp then he cannot perform effectively.
Obama loss my support for the next elections. If he can't take critizied then he shouldn't take this job. The thing is the situations is not going to get better there. He forgot about the freedom of speech.
I so agree Lekylou!
It's not against the law for someone in the military to state an opinion or disagree with a policy, unless those statements are criminal in nature....& I don't believe the statements McChrystal's staff made fall in that category. He should've been reprimanded for the embarrassment to the Oval office, certainly – but not fired. Just my opinion, as a citizen in this free country.
Obama just makes it more clear that he is the wrong man in the wrong job at the wrong time and he is not good for this country during the time of fiscal instability, wars on foreign shores and healthcare in shambles. I had such hopes but it is clearly apparent that Obama's feelings get hurt and he retaliates . . . the only good thing is that I feel he has assured America he is a one-term president. I am also disappointed in Robert Gates and I have thought he was the best thing to happen to the cabinet in a long time. In fact, I hope Gates would be the president's running mate next time around. BIden should be put out to pasture.
If the obstructionist team of McConnell, Boehner and Cantor would quit blocking everything the President to trying to accomplish the country would be in far better condition. Even with all the objections of the GOP who place party above country, this President has accomplished more GOOD in 18 months than Bush did in 8 years. Under Obama more al-Queda and Taliban leaders have been caught or killed. Winding down the wars with the one in Iraq based on Bush lies. He has started the process of financial reform. For those of us who lost huge amounts of our retirement funds due to lack of oversight of the financial sectors, this move is great. Why should people be denied medical insurance or have to pay outrageous preminums because of a precondition? My nephew had a condition that has shown no sign of recurrence for over 10 years but his insurance premium is $20,000 annually. He has to maintain two jobs to cover his insurance. You may think that is okay. I don't. Obama has restored our standing with Europe which was greatly damaged under Bush. He inherited a huge deficit from an ENORMOUS surplus. He acted to save the American automotive industry. The list goes on.
So, what is your problem? Actually, that is a rhetorical question as the answer is easy. You are uninformed.
Freedom of Speech is limited when you're in the military. You lose certain rights.
It is inexcusable for Pentagon employees to reveal confidential material to the press. General McChrysal showed a huge lack of maturity and insubordination by his words and actions. To have kept him would undermine the office of the President (this is a bigger issue than McChrystal and Obama). You cannot have active military personnel going around making fun of the President, VP, NSA (General Jones), Ambassadors and other high ranking officials of the administration. There are Representatives like Cantor who wanted the President to keep McChrystal. Why? So the GOP could claim the President is weak. For this country to move ahead there has to be a lot less polarization - and polarization seems to be the major goal of the GOP. Party above country.