The FBI is making a new push to determine how a woman who had an affair with retired Gen. David H. Petraeus when he was CIA director obtained classified files, part of an expanding series of investigations in a scandal that also threatens the career of the United States’ top military commander in Afghanistan.

Senior law enforcement officials said that a late-night seizure on Monday of boxes of material from the North Carolina home of Paula Broadwell, a Petraeus biographer whose affair with him led to his resignation last week, marks a renewed focus by investigators on sensitive material found in her possession.

“The issue of national security is still on the table,” one U.S. law enforcement official said. Both Petraeus and Broadwell have denied to investigators that he was the source of any classified information, officials said.

The surprise move by the FBI follows assertions by U.S. officials that the investigation had turned up no evidence of a security breach — a factor that was cited as a reason the Justice Department did not notify the White House before last week that the CIA director had been ensnared in an e-mail inquiry.

The disclosure about the FBI’s renewed focus comes as investigations of the matter expanded on other fronts.

The Defense Department said Tuesday that its inspector general is examining hundreds of e-mails between Marine Gen. John R. Allen, the U.S. commander in Afghanistan, and a Florida woman also linked to the Petraeus inquiry.

At the same time, key lawmakers signaled their intent to scrutinize the Justice Department’s handling of an inquiry that focused initially on a potential conflict between two private people but quickly morphed into an examination of the e-mail of two top national security officers.

“My immediate gut is like this is the National Enquirer,” Sen. Dianne Feinstein (D-Calif.), the chairman of the Senate intelligence committee, said in an interview on CNN. “I mean, every day there is something new.”

Feinstein added that she has “many questions about the nature of the FBI investigation, how it was instituted, and we’ll be asking those.”

White House spokesman Jay Carney said that President Obama maintains confidence in Allen and that the four-star general will continue to lead the war in Afghanistan even as he faces the inspector general’s inquiry.

“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,” Carney said, adding that Obama “has faith in General Allen, believes he’s doing and has done an excellent job.”

At the same time, Carney said Obama put on hold Allen’s nomination to serve as supreme allied commander for NATO forces in Europe, canceling Allen’s appearance before the Senate Armed Services Committee this week.

The Allen investigation focuses on his extensive correspondence with Jill Kelley, a Tampa resident who had carved out a role as an ad hoc social ambassador to military personnel at MacDill Air Force Base.

Kelley, 37, a close friend of Petraeus and Allen, inadvertently triggered the investigation that led to Petraeus's resignation after Allen forwarded her anonymous e-mails he had received from someone using the handle “kelleypatrol.” The messages warned Allen to stay away from Kelley, calling her a “seductress” and suggesting that Petraeus was having an intimate relationship with her, according to a source close to Kelley.

Kelley subsequently received additional e-mails in a similar vein, sent to an account she shared with her husband. The source close to Kelley said they were sent under four anonymous names, some apparently from Internet cafes. Kelley shared the initial e-mails forwarded from Allen with a friend who is an FBI agent, and eventually turned over all the missives to the bureau, which determined that Broadwell had sent them. The subsequent FBI inquiry exposed the Broadwell-Petraeus affair.

Close associates of Allen, who is married, said the general denied that he had an affair with Kelley or that he had committed any wrongdoing in his communications with her. One said that investigators may have misconstrued platonic references to her as a “sweetheart.”

Nevertheless, the bureau turned over a mountain of documents to Pentagon officials — an estimated 20,000 to 30,000 pages, based largely on communication between Allen and Kelley — prompting Defense Secretary Leon E. Panetta to order an inspector general inquiry.

The FBI inquiry of Broadwell and the new Pentagon probe of Allen create the potential for more evidence to surface, and for the scandal to expand further.

The sequence of events, and the seemingly belated disclosures that Petraeus and Allen had been ensnared in the same investigation, have placed scrutiny on the Justice Department and the FBI.

The inquiry had been underway for months before the FBI notified the director of national intelligence on election night last week that the bureau had uncovered evidence that the CIA director was having an affair.

The Allen e-mails surfaced as part of the same inquiry over the summer, but notification of his involvement came even later. Carney said that the White House was not aware of the “situation” regarding Allen until Friday, adding that the revelations about the general and Petraeus stunned the president. “I certainly, I think, wouldn’t call it welcome,” Carney said.

Defense officials said the FBI contacted Jeh Johnson, the Pentagon’s top counsel, Sunday afternoon. He then called Jeremy Bash, Panetta’s chief of staff, who was flying with his boss to Asia. Within 24 hours, Panetta approved an inspector general investigation.

“It wasn’t instant anger,” the senior defense official said of Panetta’s immediate reaction. “Panetta was concerned when he heard the news. He knew he had to follow the appropriate process. He has great respect for General Allen. He was saddened at what he knew was coming down the pike.”

A senior Senate aide said the Senate Armed Services Committee wasn’t notified until about 9 p.m. Monday, when the Pentagon asked the panel to postpone a scheduled confirmation hearing for Allen this week. At the same time, the committee was asked to move “expeditiously” to confirm Gen. Joseph F. Dunford Jr., who has been nominated to succeed Allen in Afghanistan.

The Senate aide said that the Pentagon provided limited information on the nature of the Allen e-mails but that the decision to investigate suggests that defense officials see no conclusive evidence of wrongdoing. “Obviously, they think that the contents of all these e-mails are at the least ambiguous,” the aide said. “But if they thought that it was clear and pointed to evidence of an affair, I assume they would withdraw his nomination and relieve him.”

Adultery is banned under military code.

Law enforcement officials offered conflicting accounts of the significance of the FBI’s seizure of materials from Broadwell’s home. Officials said Broadwell provided access to the residence, which the FBI requested on Sunday, and turned over computers, files and other material. She was not present when the search occurred over several hours Monday night.

A second U.S. law enforcement official acknowledged that investigators remain focused on determining whether classified material was compromised but that more serious threats were ruled out. One official called the search a “clean-up effort” in the wake of congressional questions and publicity to ensure that the FBI had not missed any classified documents in its initial search or the significance of items already examined and discussed with her.

After investigators found ­e-mails linking Broadwell and Petraeus, their initial focus over the summer was whether the CIA director’s “e-mail had been hacked, he was in danger, or he was compromised,” the official said.

The ongoing effort is now aimed mainly at Broadwell. It “is now about the source of documents on her computer,” the official said. “At this point, there is no evidence to support that [Petraeus] was the source.” The official added that it would be a “little breathless to describe it as a national security investigation.”

Broadwell, a West Point graduate and former Army officer, previously had a security clearance, although personal possession of classified files could still be a crime. The probe is being run by the cybercrime unit of the Tampa FBI field office, officials said.

The developments have complicated the administration’s attempt to contain the political fallout from the attack on a U.S. diplomatic outpost in Benghazi, Libya, in September that killed four Americans.

Feinstein and Sen. Susan Collins (Maine), the ranking Republican on the Senate Homeland Security and Governmental Affairs Committee, said Tuesday that Petraeus is still likely to be called to testify on the CIA’s involvement in the incident and its aftermath.

“I think it is absolutely imperative that General Petraeus come and testify,” Collins said. “He was CIA director at the time of the attack. He visited Libya after the attack. He has a great deal of information that we need in order to understand what went wrong.”

Petraeus had been scheduled to testify to Congress on Thursday about the Benghazi attack, but the agency will now be represented in closed-door hearings by its acting director, Michael J. Morell.

Craig Whitlock, traveling with Panetta; Ernesto Londoño in Tampa; and Anne Gearan, Julie Tate, Kimberly Kindy and Ed O’Keefe in Washington contributed to this report.