But the president said he is reserving judgment about how the FBI has handled the investigation that began in the summer but didn't reach his desk until after last week's election.
"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 when Tampa, Fla., socialite Jill Kelley turned over anonymous emails that had been sent to her and Gen. John Allen, the top U.S. commander in Afghanistan. The first anonymous email was sent to Allen in May, under the pseudonym "Kelleypatrol," and he forwarded it to Kelley.
That email warned Allen to stay away from Kelley, according to a person close to Kelley who spoke on condition of anonymity because the investigation into the emails is ongoing. That same email -- later traced to Broadwell -- said the writer knew about a future meeting Allen and Kelley had scheduled. Allen thought the email was a joke or that it was possibly from Kelley because he didn't know how anyone else would know about their planned meeting, the person close to Kelley said.
Kelley was a friend of Allen and Petraeus, both of whom she had met in Tampa when the men served there.
One of the federal law enforcement officials confirmed Wednesday that FBI agents were concerned that somebody was tracking the movements of Allen and Petraeus, raising the possibility of a national security breach.
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 said Broadwell apparently saw Kelley as a rival for Petraeus' affections.
The official also said Wednesday that Broadwell sent emails to a couple of other senior military officials besides Petraeus and Allen. The official characterized the emails as an attempt to undermine Kelley's reputation.
The FBI found a substantial number of classified documents on Broadwell's computer, and she has told agents that took classified documents out of secure government buildings, according to the official.
On Monday, the FBI also found classified documents in the search of Broadwell's house in Charlotte, N.C., the official said. Broadwell had agreed to the search and had told agents in advance that there would be more of them there.
A lawyer for Allen released a statement promising the general would cooperate fully with the Defense Department inspector general's investigation.
"To the extent that there are questions about certain communications by General Allen, he shares in the desire to resolve those questions as completely and quickly as possible," said Col. John Baker, chief defense counsel of the Marine Corps. Allen has denied any wrongdoing.
In early June, Kelley herself received the first of as many as five emails sent from different anonymous accounts alleging that she was up to no good, the person close to Kelley said. One of those mentioned Petraeus by name. By the end of June or early July, Kelley contacted an FBI agent in Tampa she had met at least a year earlier, which began the agency's investigation of the matter. The New York Times identified the agent as Frederick W. Humphries, 47, a veteran counterterrorism investigator in the Tampa office.
Kelley met Humphries when she attended the bureau's Citizens' Academy, an FBI program aimed at showing members of the public at least some of what the FBI does and how it works, the person close to Kelley said.
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.
Separately, a U.S. official said the Army has suspended Broadwell's security clearance. As a former Army intelligence officer, she held a high security clearance. The official spoke on condition of anonymity because the source was not authorized to discuss the matter publicly.
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.
Petraeus will testify Friday before the House Intelligence Committee about Libya, panel spokeswoman Susan Phalen 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."
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.
Associated Press Kimberly Dozier, Pauline Jelinek, Lolita Baldor, Michael J. Sniffen, Eileen Sullivan and Adam Goldman in Washington and Dale Wetzel in Bismarck, N.D., contributed to this report.
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