America's top law-enforcement agency found itself under intense scrutiny as it was alleged that one if its field agents had become obsessed with Jill Kelley, the 37-year-old party organiser from Florida who was bombarded with threatening emails from Paula Broadwell, Mr Petraeus's mistress.
Tomorrow members of the House intelligence committee are expected to grill Sean Joyce, the FBI's deputy director, and Michael Morell, Mr Petraeus's replacement as head of the CIA, demanding to know why his agency's investigation into the former CIA director and four star general was kept secret until the day of the presidential election.
Peter King, a Republican member of the committee, said it was "inexcusable" that the FBI had waited for months to inform the White House that it was looking into a key member of Mr Obama's national security team.
"Whenever General Petraeus's name came up I believe the FBI had an absolute obligation to tell the White House, and specifically the President, what this involved," Mr King said.
FBI agents also abruptly searched Mrs Broadwell's home in North Carolina as they continued to hunt for any evidence that the sex scandal could have led to a breach of national security.
The bureau's involvement with the affair began in Tampa over the summer, when Mrs Kelley told a friend in the FBI she was receiving anonymous messages accusing her of inappropriate flirting with Mr Petraeus.
The unnamed agent carried her concerns to the local field office, where investigators began a routine cyber harassment investigation that quickly escalated after they realised they had stumbled over evidence that the then-director of the CIA was having an extramarital affair.
Unbeknown to senior FBI officials, however, the agent allegedly had a history of infatuation with Mrs Kelley, a married mother-of-three, and had earlier sent her photographs of himself shirtless.
Supervisors became concerned about his near-obsession with the case and decided to pull him off the investigation and refer him to the bureau's internal affairs unit, according to the Wall Street Journal.
The agent reportedly became convinced that the FBI was stalling the investigation in order to protect President Barack Obama from political embarrassment and took it on himself to leak details to Eric Cantor, the second most senior Republican in the House of Representatives.
Mr Cantor contacted the FBI on October 31 – a week before anyone outside the Justice Department was officially told about the investigation – but did not go public with the information out of concern about the reliability of the source.
The FBI has refused to officially comment on the decision to keep the investigation secret, but in private briefings has insisted that there was no obligation to pass information on because it had already determined that there was no breach of national security.
However, the FBI had already discovered classified information on Mrs Broadwell's computer and investigators returned to her house in a wealthy suburb of Charlotte, North Carolina, late on Monday night.
Mrs Broadwell, 40, her husband, and two children were not at home but officials said the search was "consensual".
Both Mrs Broadwell and Mr Petraeus, 60, have denied that he gave her the classified documents and charges are not expected against either.
The FBI did not return multiple calls requesting comment.