WASHINGTON FBI Director Robert Mueller’s top aide was told former CIA chief David Petraeus was having an extramarital affair that might have compromised national security a week before the Nov. 6 elections, a congressional official said Monday.

The disclosure raises fresh questions about why the FBI leadership withheld the information from the nation’s top intelligence official and the congressional committees that oversee the U.S. intelligence community until after President Barack Obama won re-election.

Had the affair that forced Petraeus’ startling resignation on Friday become public earlier, it might have stoked a political outcry already flaring over the deaths of the U.S. ambassador to Libya, two CIA contractors and a State Department staffer in a Sept. 11 attack on the U.S. consulate in Benghazi, Libya, by suspected Islamist extremists.

Meanwhile, new reports reveal that Petraeus told Paula Broadwell of Charlotte, with whom he was having an extramarital affair, to stop sending threatening emails to a family friend, Jill Kelley, after a federal investigation determined who was behind the harassment.

The FBI investigation that uncovered the affair began after Kelley, of Tampa, Fla., complained to an FBI agent, a personal friend, about what she considered threatening emails from an anonymous sender.

The emails reportedly accused Kelley, who became friends with Petraeus and his wife while the general served as head of the Tampa-based U.S. Central Command, of improper behavior with Petraeus.

The sender was eventually identified as Broadwell by FBI investigators, who found emails in her inbox that led them to conclude that she was having an affair with Petraeus. An FBI spokesman on Friday emphasized that Petraeus is not the target of any criminal probe or charges.

People close to Petraeus say his affair with Broadwell ended four months ago, around the time he emailed her about the harassment.

Spokesman: End was mutual

Petraeus, 60, and Broadwell, 40, began their affair about two months after he became CIA director in September 2011, and they had agreed to end it about four months ago, said retired Army Col. Steve Boylan, a former Petraeus aide who is acting as his unofficial spokesman.

“There weren’t a lot of meetings,” Boylan told McClatchy. “Based on what I understand, it was a mutually agreed upon realization that this was something they shouldn’t be doing.”

Petraeus and Broadwell apparently used a trick to conceal their email traffic, a law enforcement official told The Associated Press.

Rather than transmitting emails to the other’s inbox, they left messages in a draft folder or in an electronic “dropbox,” the official said. Then the other person could log on to the same account and read the emails there. This avoids creating an email trail that is easier to trace.

Petraeus was informed of the FBI investigation at, or just before, the beginning of November, and told his wife of 38 years, Holly, just before he sent a statement to the CIA workforce on Friday, admitting to adultery and announcing that he was resigning, Boylan said.

“They are a very strong family. He has done a pretty bad thing and hurt them deeply,” he said. “But given time and space, they can get through it.”

Boylan denied that Petraeus ever passed classified information to Broadwell.

“The two were separate,” he said. “One was his private life. One was his professional career, which came to an end on Friday, at least for now.”

Broadwell, a West Point graduate and Army reservist, is married with two children.

‘A very formulaic answer’

It remained unclear on Monday at what point Attorney General Eric Holder and FBI Director Mueller were officially notified by their subordinates of the investigation’s findings.

In late October, Republican Rep. Dave Reichert of Washington state received a tip from an FBI source that the CIA director was involved in an affair. Reichert arranged for an associate of his source at the FBI to call House Majority Leader Eric Cantor on Oct. 27, according to Cantor spokesman Rory Cooper. Cooper told McClatchy that an FBI agent informed the lawmaker of an affair involving Petraeus and “warned that national security or classified information may be compromised.”

The agent who contacted Reichert was the same one who first received the allegations about harassing emails from Kelley and passed them along to the FBI, a federal law enforcement official told The Associated Press Monday night. The agent was subsequently told by his superiors to steer clear of the case because they grew concerned that he had become obsessed with the investigation, the official said. The agent was a friend of Kelley, and long before the case involving Petraeus got under way, had sent Kelley shirtless photos of himself, according to this official.

Cantor and his chief of staff, Steve Stombres, decided the following day to contact Mueller’s office. Hurricane Sandy, however, struck that evening, shutting down Washington and forcing them to delay the call until Oct. 31, when Stombres spoke to Mueller’s chief of staff, Aaron Zebley, Cooper said.

The FBI told Stombres the following day that it couldn’t confirm or deny the investigation that uncovered the affair, but emphasized that national security and classified information were top priorities for the bureau.

It was “a very formulaic answer,” said Cooper.

FBI spokesmen didn’t immediately respond to emailed questions about whether Zebley informed Mueller of Stombres’ call, or when Mueller first learned of Petraeus’ affair or the investigation that uncovered it.

The New York Times on Monday reported that the FBI didn’t conclude that Petraeus hadn’t committed a crime until after interviewing Broadwell for a second time on Nov. 2. Bureau officials then informed Director of National Intelligence James Clapper, who oversees the 16 U.S. intelligence agencies, of the affair about 5 p.m. on Election Day.

Clapper asked Petraeus on the following day to resign. The former general submitted his resignation on Thursday to Obama, who took until the following day to accept it.

Broadwell’s surprising claims

During a talk last month at the University of Denver, Broadwell raised eyebrows when she said the CIA had detained people at a secret facility in Benghazi, Libya, and the Sept. 11 attack on the U.S. Consulate and CIA base there was an effort to free those prisoners.

Obama issued an executive order in January 2009 stripping the CIA of its authority to take prisoners. The move meant the CIA was forbidden from operating secret jails across the globe as it had under President George W. Bush.

CIA spokesman Preston Golson said: “Any suggestion that the agency is still in the detention business is uninformed and baseless.”

Broadwell did not say who told her about CIA activities in Libya. The video of Broadwell’s speech was viewed on YouTube.

Questions remain

The federal government was closed Monday for Veterans Day, but the White House, the Justice Department and the FBI were expected to come under intense pressure from Congress, the news media and the public on Tuesday about when they first learned of the affair.

Some senior lawmakers want to know why they weren’t told about the matter until Friday. Legal requirements mandate that congressional oversight committees be kept informed of all intelligence activities, including possible compromises of national security and classified information.

The FBI and the Justice Department, however, also are subject to privacy considerations and rules protecting people involved in investigations who have been found not to have violated any laws.

As the nation’s top spy, Petraeus was one of the most closely protected senior U.S. officials. A security team guards him around the clock, manning a command center at his home, said a former senior intelligence official, who requested anonymity in order to speak freely. On overseas trips, the team stays in the rooms on either side of the director’s room and keeps his door under constant surveillance.

“They’d know who was going into the room, but they wouldn’t know what was going on behind the closed door,” he said. The Washington Post and Associated Press contributed