"I have a lot of confidence, generally, in the FBI," Obama said, qualifying his words of support for the agency and its actions in the case.
As Obama spoke about the scandal from the White House, legislators on Capitol Hill were grilling FBI and CIA officials privately about the same issues: whether national security was jeopardized by the case and why they didn't know about the investigation sooner.
"I have no evidence at this point, from what I've seen, that classified information was disclosed that in any way would have had a negative impact on our national security," Obama said at his first postelection news conference.
As for the FBI's handling of the matter, Obama said: "My expectation is that they follow the protocols that they've already established. One of the challenges here is that we're not supposed to meddle in criminal investigations, and that's been our practice."
Federal law enforcement officials have said the FBI didn't inform the White House and Congress sooner about the original investigation because of rules set up after the Watergate scandal to prevent interference in criminal investigations, and that lawmakers weren't given notice of potential national security problems because the bureau had quickly resolved them.
CIA Director David Petraeus resigned Friday, two days after the White House was notified that he'd acknowledged having an affair with his biographer, Paula Broadwell.
The FBI's investigation of the matter began last summer, after Broadwell allegedly sent harassing, anonymous emails to a woman she apparently saw as a rival for Petraeus' affections. That woman, Florida socialite Jill Kelley, in turn had traded sometimes-flirtatious messages with the top U.S. commander in Afghanistan, Gen. John Allen.
Kelley's complaints about the threatening emails triggered the FBI investigation that led to the resignation of Petraeus and the inquiry into her communications with Allen.
Officials who have seen the communications between Allen and Kelley on Wednesday described some of the emails as "suggestive," and said their release would be embarrassing for the general. The officials spoke on condition of anonymity because they were not authorized to discuss the situation publicly.
With Broadwell and Kelley suddenly in the center of the storm, small details suddenly became topics for discussion.
Word surfaced Wednesday that Kelley's pass to enter MacDill Air Force Base in Florida had been indefinitely suspended, a decision made at the base level. Pentagon spokesman Lt. Col. Steven Warren said Kelley still can enter the base but must report to the visitor center and sign in like others without a pass.
Broadwell, who lives in Charlotte, N.C., was spotted in Washington at her brother's home late Tuesday. Her listing in her high school yearbook in Bismarck, N.D., as "most likely to be remembered" took on new meaning.
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 will continue on Thursday.
Rep. Dutch Ruppersberger, the top Democrat on the House Intelligence Committee, said a hearing scheduled for Thursday to explore the government's handling of the attacks on the U.S. Consulate in Benghazi, Libya, also would touch on the Petraeus affair, covering how and why the FBI investigation was started. He said Mueller, Joyce and Morell only began to answer those questions Wednesday.
"How did you get the information, what's the basis for the investigation, who did you talk to, were you working with prosecutors, all those issues have to be looked at," including why the intelligence committees weren't told of the investigation until just before Petraeus' resignation, he said.
Lawmakers are also concerned over reports that Broadwell had classified information on her laptop, though FBI investigators say they concluded there was no security breach.
FBI agents who contacted Petraeus told him that sensitive, possibly classified documents related to Afghanistan were found on her computer, the general's associates said. He assured investigators they did not come from him, and he mused to his associates that they were probably given to her on her reporting trips to Afghanistan by commanders she visited in the field there.
One associate also said Petraeus believes the documents described past operations and had already been declassified, although they might have still been marked "secret."
Broadwell had high security clearances as part of her former job as a reserve Army major in military intelligence. But those clearances are only in effect when a soldier is on active duty, which she was not at the time she researched the Petraeus biography.
Feinstein, asked by reporters if there was a national security breach with the Petraeus affair, said she had "no evidence that there was at this time."
Feinstein said that Petraeus himself would testify before Congress — but not about the affair. She said he had agreed to appear to talk about the Libya attack on Sept. 11 that killed the U.S. ambassador and three other Americans, but she said no date had been set.
Allen has been allowed to stay in his job as commander of the Afghan war, providing a leading voice in White House discussions on how many troops will remain in Afghanistan — and for what purposes — after the U.S.-led combat operation ends in 2014.
But 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 20,000-plus pages of documents and emails that involve Allen and Kelley.
Defense Secretary Leon Panetta, at a news conference in Perth, Australia, said, "No one should leap to any conclusions" about Allen, and said he is fully confident in Allen's ability to continue to lead in Afghanistan. He added that putting a hold on Allen's European Command nomination was the "prudent" thing to do.
NATO Secretary-General Anders Fogh Rasmussen said he had "full confidence" in Allen and looked forward to working with him if he is ultimately confirmed.
The Senate Armed Services Committee planned to go ahead with Thursday's scheduled confirmation hearing on the nomination of Marine Corps Gen. Joseph Dunford, who is to replace Allen as commander of U.S. and NATO forces in Afghanistan, if Allen is indeed promoted.