Washington was in shock Saturday after the sudden resignation of CIA chief and ex-US commander in Iraq and Afghanistan, David Petraeus, handing another major challenge to President Barack Obama just three days after his re-election.

Petraeus said he resigned over an extramarital affair, bringing an ignomious end to a highly praised military and government career. It also came shortly before the US spy chief had been due to testify in Congress on the agency’s alleged failure to protect a US consulate in Libya from a deadly attack.

“After being married for over 37 years, I showed extremely poor judgment by engaging in an extramarital affair,” the CIA director said in a message to staff, released to the media Friday.

Obama, in a written statement, acknowledged Petraeus’s departure, praising his “intellectual rigour, dedication, and patriotism.”

But at the same time, he expressed confidence that the Central Intelligence Agency “will continue to thrive and carry out its essential mission” without the famed general.

The president, fresh off his electoral triumph, reportedly had no inkling that the CIA chief was about to resign until Thursday morning.

When he met with Petraeus later that day, Obama refused to accept the resignation straight away, saying he would think about it overnight, the New York Times said.

But in the end, Obama concluded he could not push Petraeus to stay on, according to the Times.

Michael Morell, Petraeus’s deputy at the country’s lead spy agency, will serve as acting director, but there were indications he might be only a temporary choice.

Speculation on a possible successor focused on John Brennan, the White House counter-terrorism adviser and CIA veteran who has played an instrumental role in Obama’s drone war against Al-Qaeda militants.

Neither Petraeus nor the CIA explained exactly why he felt he had to step down over the affair, and whether his liaison presented a purely personal problem or raised security issues in his sensitive work as spy chief.

The affair came to light as the FBI was investigating whether a computer used by Petraeus had been compromised, the New York Times and other US media reported, citing government officials.

NBC News and other media reported the Federal Bureau of Investigation was investigating Paula Broadwell, co-author of a favourable biography of Petraeus, “All In: The Education of David Petraeus,” for possible improper access to classified information.

Unnamed officials told the New York Times that Petraeus’s lover was Broadwell, a former Army major who spent long periods interviewing Petraeus for her book. She offered no public comment on the revelations.

Experts noted that if Petraeus, a four-star general who retired to take the CIA job, had committed adultery while still in the army, he could have been court-martialed.

The resignation comes amid criticism in some quarters of Petraeus over his response to the deadly attack in September on the US consulate in Benghazi, which killed the US ambassador to Libya and three other Americans.

Intelligence officials have defended Petraeus and his officers over the incident, saying the CIA moved swiftly to rescue the Americans under attack at the Benghazi compound.

The most celebrated military officer of his generation, Petraeus, 60, took over at the CIA a little over a year ago. He was credited by some with rescuing a failing US war effort in Iraq in 2007, after then president George W. Bush ordered a surge of troops into the country.

Obama later turned to him to lead a similar surge of American forces in Afghanistan in 2010, leaving a top post as commander of all US forces in the Middle East to do so.

But Obama chose not to promote Petraeus to the US military’s top job as chairman of the Joint Chiefs of Staff, as White House officials remained wary of the media-savvy general who had pushed for more troops and more time in the Afghanistan war.

His military background, however, sometimes clashed with the intelligence agency’s culture and there was some friction with the congressional committees that oversee the spy services.

After accepting the CIA chief’s resignation, Obama hailed his “extraordinary service.”

At the CIA, he had worked to shift the spy agency to a more “balanced” approach to intelligence gathering, after an intense focus on terror threats after the 11 September, 2001 attacks, said Bruce Riedel, a former CIA officer and fellow at the Brookings Institution think tank.

“He had already begun to position the agency to live in the post-9/11 world,” he told AFP.

Senator John McCain, a loyal supporter who championed the general’s surge strategy in Iraq, heaped praised on Petraeus.

“General David Petraeus will stand in the ranks of America’s greatest military heroes,” he said.

Petraeus has long been suspected of harbouring political ambitions but he has repeatedly fended off questions about a possible White House run.

Intensely competitive and known for his sharp intellect, he graduated from the US Military Academy at West Point in 1974, where he met his wife, Holly, the daughter of West Point’s superintendent. The couple has two children.