Obama keeps 'faith' in US Afghan commander Allen

President Barack Obama has "faith" in General John Allen to remain in command of US forces in Afghanistan while he is investigated for alleged inappropriate behavior, the White House said today.

White House spokesman Jay Carney also said Obama was "surprised" when he learnt about CIA chief David Petraeus' extramarital affair, but had confidence in deputy director Michael Morell to run the agency as interim head.

"I can tell you that the president thinks very highly of General Allen and his service to his country, as well as the job he has done in Afghanistan," Carney said in response to a question about a Pentagon probe into reports that Allen sent hundreds of "flirtatious" emails to a married woman.

"He has faith in General Allen, believe he is doing and has done an excellent job at ISAF," he added, referring to the US-led NATO mission in Afghanistan, which Allen has led since July last year and is due to leave in January in order to become the alliance's supreme commander.

Carney refused to comment on the investigation into Petraeus, who resigned after confessing to an affair with a 40-year-old reservist officer who wrote a biography of him, referring reporters to the FBI and Justice Department.

"Well the president was certainly surprised when he was informed about the situation regarding General Petraeus on Thursday," Carney said.

"He greatly appreciates General Petraeus' remarkable service to his country both in uniform and at the CIA. And his thoughts and prayers go out to both General Petraeus and Holly Petraeus," he added, referring to Petraeus' wife.