According to reports, Petraeus's affair was exposed when the FBI investigated threatening emails from his lover to a mystery second woman.
Republicans, meanwhile, demanded more answers, pointing to the fact that Petraeus had been days away from testifying about the September 11 attack on the US consulate in Benghazi, Libya smacked of some kind of conspiracy.
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 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 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 indicated that she thought the other woman was a potential rival for the 60-year-old general's affections, anonymous law enforcement officials told the Washington Post.
Both newspapers said the mystery woman was not Petraeus's wife or a member of his family, but someone close to the general who does not work for the Central Intelligence Agency.
The recipient of the emails was so frightened, according to the 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 there may have been a national security breach with someone breaking into the CIA chief's private email account.
Investigators first interviewed Petraeus "about two weeks ago," law enforcement officials told the Post.
A leading Republican questioned why, if there were serious concerns about comprised intelligence, it took several months for the FBI to finally notify the Obama administration.
Obama's director of national intelligence James Clapper was only informed of the situation on Tuesday evening.
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 wasn't told until Thursday morning, according to the White House.
Some Republicans have sought to draw a connection between the timing of Petraeus's resignation and his scheduled appearances before Congress on Thursday to answer questions related to another brewing scandal.
"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 analysed to see what happened."
Petraeus had been due to testify about the attacks in Benghazi that killed Ambassador Chris Stevens and three other Americans.
CIA deputy director Michael Morell, promoted suddenly to acting director because of the Petraeus scandal, is now scheduled to appear instead.
The head of the Senate intelligence committee, Democrat Dianne Feinstein, told Fox News Sunday that 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 Defence 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.
Others include Michael Vickers, undersecretary of defence for intelligence, and Congressman Michael Rogers, a Republican who heads the House intelligence committee.
The most celebrated military officer of his generation, Petraeus took over at the CIA a little more than a year ago. He was credited by some with rescuing a failing US war effort in Iraq with the 2007 surge.
Obama later asked Petraeus to lead a similar surge of US forces in Afghanistan in 2010 which has had more questionable success.
Petraeus explained his resignation to CIA staff in simple terms 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," he said. "Such behaviour is unacceptable, both as a husband and as the leader of an organisation such as ours." – Sapa-AFP