After announcing he will nominate Petraeus, who is the immediate superior to McChrystal, Obama urged Congress to confirm the nomination as soon as possible. Petraeus served as commander of U.S. forces in Iraq during former President George W. Bush's troops surge there.

The U.S. and NATO commander in Afghanistan U.S. General Stanley McChrystal wears earplugs as he leaves by helicopter after a meeting between Afghan President Hamid Karzai and tribal leaders in Kandahar city June 13, 2010. [Xinhua]

McChrystal was summoned to Washington to explain his remarks critical of Obama and other senior administration officials. He met with Gates in the Pentagon in the early morning, and then with Obama in the White House. Both meetings lasted around half an hour.

McChrystal was initially expected to join the monthly strategy meeting of Obama's Afghan war advisers in White House situation room, but he was not seen returning to the White House after the morning meeting with Obama.

McChrystal made the disparaging remarks to the Rolling Stone magazine. In a profile titled Runaway General, which is to appear in this week's magazine, McChrystal said he felt betrayed by U.S. ambassador to Kabul Karl Eikenberry. He recalled to the magazine the time he asked for more troops from Obama as "painful," and said Obama had him in "an unsellable position" to ask for an increase in troops.

Obama eventually decided to send 30,000 more troops to Afghanistan in December.

The magazine story also contained mocking remarks from McChrystal's inner circle of aides towards senior administration officials such as Biden and National Security Adviser James Jones.

After Obama made the remarks, McChrystal released a statement saying he offered his resignation out of a desire to see the mission in Afghanistan succeed, and he supports Obama's strategy and remains deeply committed to the war.

Afghan President Hamid Karzai, who voiced his support to McChrystal earlier, said through a spokesman he respects Obama's decision, and looks forward to working with Petraeus.

NATO Secretary General Anders Fogh Rasmussen said in Brussels the coalition's strategy in Afghanistan remains unchanged.