Broadwell was granted unprecedented access to the general as she co-authored his biography
The FBI uncovered the affair that led to the resignation of CIA chief David Petraeus while investigating threatening emails sent by his lover to a second woman, US media reported.
Petraeus, an American hero credited with turning the tide of the Iraq war, resigned on Friday after admitting an extramarital affair, sending shockwaves around Washington just three days after President Barack Obama's re-election.
It has emerged that his paramour was Paula Broadwell, a 40-year-old former Army major granted unprecedented access to the general as she co-authored a best-selling biography: "All In: The Education of General David Petraeus."
Newspaper reports on Sunday revealed that the affair came to light when the FBI was called in as part of a criminal investigation launched when a second woman complained that she had received vicious emails from Broadwell.
"It didn't start with Petraeus, but in the course of the investigation they stumbled across him," an unnamed congressional official briefed on the matter told The New York Times.
The threatening and harassing emails from Broadwell, a married mother of two, indicated that she thought the other woman was a potential rival for the 60-year-old general's affections, officials told the US media.
A government official told The New York Post that the emails contained such language as: "I know what you did," "back off" and "stay away from my guy."
AP, citing a senior US military official, identified the other woman as 37-year-old Jill Kelley, a "social liaison" to a Florida air force base who apparently had a longstanding friendship with Petraeus but no official status in the military. She was earlier identified as a State Department liaison.
The recipient of the emails was so frightened, according to the Washington Post, that several months ago she went to the FBI for protection and to help track down the sender.
The FBI soon uncovered Broadwell's sexually explicit correspondence with Petraeus, leading to initial fears of a national security breach if someone had broken into the CIA chief's private Gmail account.
Investigators first interviewed Petraeus "about two weeks ago," law enforcement officials told the Post.
The FBI has concluded that there will not be criminal charges, US media reports said, citing law enforcement sources.
Obama's director of national intelligence James Clapper was only informed of the situation on Tuesday evening, providing a dramatic behind-the-scenes backdrop to the president's re-election night. Clapper discussed things with Petraeus on Wednesday and advised him "the right thing to do would be to resign," an intelligence official told the Times. Obama was not told until Thursday morning, the White House said.
Senior FBI and CIA officials are set to brief top lawmakers on Capitol Hill on Tuesday about their investigation.
The US government is closed on Monday as part of the Veterans Day holiday. But on Tuesday, when the government reopens, senior FBI and CIA officials were scheduled to meet with leading members of Congress to bring them up to date about details of the probe, media reports said.
Republicans have pointed to the fact that Petraeus was days away from testifying about the September 11 attack on the US consulate in Benghazi, Libya as evidence of some kind of conspiracy.
A leading Republican questioned Sunday why, if there were serious concerns about comprised intelligence, it took several months for the FBI to finally notify the Obama administration.
"It just doesn't add up," Peter King, the top Republican on the House Homeland Security Committee, told CNN. "I have real questions about this. I think a timeline has to be looked at and analyzed to see what happened."
Petraeus had been due to testify on Thursday about the Benghazi attacks that killed Ambassador Chris Stevens and three other Americans. CIA deputy director Michael Morell, now acting director, will testify in his place.
The chairwoman of the Senate intelligence committee, Democrat Dianne Feinstein, told "Fox News Sunday" she was angry at not being informed earlier and said Petraeus "may well" still be called at a later date.
The stunning departure of Petraeus has left Obama with an added headache as he begins his second term.
The president will likely have to replace not only departing Secretary of State Hillary Clinton, but also Defense Secretary Leon Panetta and Treasury Secretary Tim Geithner.
One name being floated as a possible Petraeus replacement is John Brennan, the White House counter-terrorism adviser and a CIA veteran who has played an instrumental role in Obama's drone war against Al-Qaeda militants.
The most celebrated military officer of his generation, Petraeus took over at the CIA a little more than a year ago.
He explained his resignation to CIA staff in a message released to the media on Friday.
"After being married for over 37 years, I showed extremely poor judgment by engaging in an extramarital affair," it said. "Such behavior is unacceptable, both as a husband and as the leader of an organization such as ours."
Broadwell lives in North Carolina with her radiologist husband Scott and their two young sons.
She planned to celebrate her 40th birthday with a big party in Washington this weekend, but her husband has now emailed guests to cancel those invitations.