The FBI also found emails between Kelley and Allen that were turned over to the Defense Department for investigation. Obama has put on hold Allen's nomination to become the next commander of U.S. European Command as well as the NATO supreme allied commander in Europe until Pentagon investigators are able to sift through the emails that involve Allen and Kelley.
Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff, said Thursday he still expects Allen to eventually take over the European Command, but acknowledged, "I see this investigation and how long it could take affecting that."
In an interview with American Forces Press Service, Dempsey said "I absolutely have confidence" in Allen's ability to continue in command in Afghanistan despite the distraction of the scandal.
Speaking at a news conference in Bangkok on Thursday, Defense Secretary Leon Panetta also said he retains confidence in Allen. He added that he knows of no other senior U.S. military officers being linked to the Petraeus investigation.
The Pentagon chief also told reporters he could not rule out the possibility that the Taliban in Afghanistan would try to use Petraeus' admission of an extramarital affair for propaganda purposes. Petraeus was Allen's predecessor as top U.S. commander in Afghanistan.
FBI Director Robert Mueller and Deputy Director Sean Joyce met privately with legislators on both sides of the Capitol on Wednesday to explain how the investigation unfolded. They met first with Senate Intelligence Committee Chairwoman Dianne Feinstein, D-Calif., and ranking Republican Saxby Chambliss of Georgia, then crossed the Capitol to meet with the House Intelligence Committee.
Acting CIA Director Michael Morell went before the House panel next, after meeting a day earlier with top Senate intelligence officials to explain the CIA's take on events that led to Petraeus' resignation.
The questioning on Capitol Hill was continuing Thursday. And Kelley's decision to contact her friend at the FBI continues to reverberate months later.
Her own pass to enter MacDill Air Force Base in Florida had been indefinitely suspended, a move that ends her easy access to the senior military officials that dot her social world.