Both Barack Obama and the Pentagon insisted on Tuesday that they were standing by the top US commander in Afghanistan, John Allen, after he became the latest general to find himself entangled in the widening Petraeus emails scandal.
Allen is under investigation by the defence department over his communications with Jill Kelley, the Tampa woman who sparked the FBI investigation that stumbled across David Petraeus' affair after she complained about "harassing" emails that were traced to his mistress Paula Broadwell.
The Pentagon's inspector general was examining 20,000 to 30,000 pages of documents, including many emails between Allen and Kelley, who has been described as an unpaid social liaison for senior officers at MacDill air force base in Tampa, home of US central command.
Asked at a White House briefing on Tuesday if the president believed Allen could continue to prosecute the war in Afghanistan while under investigation, the president's spokesman Jay Carney said: "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 … He has faith in General Allen, believes he's doing and has done an excellent job at Isaf [International Security Assistance Force]."
A Pentagon official, at a separate, anonymous briefing, said Allen denied having had an affair and that the email exchanges were at worst "flirtatious".
Allen had been scheduled to take over as chief of US forces in Europe and as the supreme commander of Nato. That appointment has been put on hold pending a defence department investigation.
The disclosures about Petraeus and Allen have disrupted president's post-election plans.
Obama was blindsided by the FBI revelations about both men.
Although there were potential national security implications at least in the case of Petraeus, Obama was not informed until last week, even though the FBI investigation had been under way for months.
Carney told reporters that Obama was first informed about Petraeus on Wednesday, the day after the election, and about Allen on Friday.
Carney did not overtly criticise the FBI but he said the president was "certainly surprised" when told Petraeus had decided to resign.
He referred detailed questions to either the Pentagon or the department of justice. Asked about the FBI delay in informing the White House, Carney said there were protocols in place the FBI had to follow. He appeared to partly contradict himself later, saying these two cases were "unique".
Suggesting a breakdown between the White House and the FBI, Carney said he was "not aware" whether Obama had spoken to the FBI director, Robert Mueller, about the investigation.
Carney admitted that he would "certainly not suggest [the president] is pleased" by these events. Asked if they had been unwelcome, he said: "Well, I certainly, I think, wouldn't call it welcome."
Allen was to have faced a Senate nominating committee this Thursday after being recommended by Obama as head of US forces in Europe and supreme commander of Nato.
A Pentagon official said that Allen had informed the chairman of the joint chiefs of staff, General Martin Dempsey, that there had been no affair and no security breach.
The emails apparently began in 2010, when Allen was in Tampa as deputy of central command, and continued through to this year.
The FBI is facing heavy criticism over its handling of the investigation, not just its failure to inform either the White House but senior members of the Senate and House intelligence committee.
Allen could face a difficult time if, after completion of a defence department investigation, he goes in front of a Senate nominating committee over the job in Europe.
He is due to be replaced in Afghanistan by General Joseph Dunford and the Obama administration has asked the Senate to agree on Thursday to his nomination promptly.
The controversies over the generals have proved a distraction in a week in which Obama had hoped to focus primarily on trying to reach a deal with Congress over debt and spending and a visit to New York still struggling to deal with the aftermath of hurricane Sandy.
They also complicate Obama's reshuffle of his cabinet and White House staff as well as filling other posts.
Obama's choice to replace Petraeus as head of the CIA could end up delayed amid messy Senate hearings depending on the choice.
Although there is a Democratic majority in the Senate, both Democrats and Republicans are united in criticism of the FBI.
Adding a further complication is that members of Congress, particularly Republicans, are still investigating what happened over the attack on the US consulate in Benghazi that left the US ambassador and three other Americans killed.
Senator Dianne Feinstein, chairwoman of the Senate intelligence committee, wants Petraeus to give evidence about Benghazi even though he has resigned from the CIA.
Benghazi could also have an impact on Obama's choice to replace Hillary Clinton, who intends stepping down as secretary of state in the second term.
Speculation about her replacement centres on the US ambassador to the UN, Susan Rice, and the Senate foreign affairs committee chairman John Kerry.
Rice could face a difficult Senate nominating process because of her involvement in the Benghazi story, having initially blamed the attack on a US-produced anti-Muslim video.
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