The sex scandal that destroyed the career of former CIA director David Petraeus continues to reverberate in Washington, jeopardising the appointment of General John R. Allen, the top allied commander in Afghanistan, to a new post as Nato's supreme commander.

The scandal has also distracted the White House as it enters negotiations with Republican Congressional leaders over the pending fiscal crisis.

It has complicated the congressional hearings into the attack in Libya that cost the lives of four Americans, including the ambassador. General Petraeus, who resigned on Saturday after confessing an affair with his biographer, was expected to appear before the hearing as CIA head this Thursday.

The Petraeus affair has also made other key defence, intelligence and diplomatic appointments more difficult. The White House must now replace General Petraeus as CIA director, but also Secretary of Defence Leon Panetta, and Secretary of State Hillary Clinton, who had already planned to stand aside when President Barack Obama named his new cabinet.

With so many senior posts to fill, the president may need to draft Senator John Kerry, who has been interested in one of the posts, forcing a special election for his seat, which could be won by the Republican Scott Brown, whittling into the Democrat's majority in the Senate.

On Friday it was revealed that the FBI's investigation into the relationship between General Petraeus and his biographer, Paula Broadwell, had uncovered a trove of up to 30,000 emails between General Allen and Jill Kelley, the Tampa socialite who sparked the original investigation when she told an FBI agent that she had received threatening emails from Broadwell, who apparently feared there was a relationship between her and General Petraeus.

This unidentified FBI agent has now become a central figure in the scandal, because it has been revealed that although he was not part of the investigation – and although it was found that no crime had been committed – he believed a cover-up was in play, and approached the Republican leader in the House of Representatives, Eric Cantor, with information about General Petraeus's affair and the FBI investigation.

It has also been reported that the FBI agent was a friend or acquaintance of Mrs Kelley's, and had once sent photographs of himself topless to her.

Meanwhile, it has been reported that General Allen denies having had an affair with Mrs Kelley.

During a White House briefing on Tuesday, the president's spokesman Jay Carney said the president still had faith in General Allen.

"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 said.

"The president remains focused on fully supporting our extraordinary troops and coalition partners in Afghanistan, who General Allen continues to lead as he has done so ably for over a year," he said.

He said he would not speculate on personnel changes.

Meanwhile, it is expected that General Petraeus will still be called upon to give evidence before a Senate hearing into the Benghazi attack.

Congressman Peter King said that the FBI should have told the White House that it was investigating General Petraeus months ago rather than last week.

Mr Carney said he believed the FBI had protocols in place over when to notify other agencies over investigations, and that they had been followed.

The Senate intelligence committee is to meet shortly to discuss the scandal.