Petraeus quit Friday after acknowledging an extramarital relationship.
The official said the FBI investigation began several months ago with a complaint against Broadwell, a 40-year-old graduate of the U.S. Military Academy and an Army Reserve officer. That probe led agents to her email account, which uncovered the relationship with the 60-year-old retired four-star general, who earned acclaim for his leadership of the wars in Iraq and Afghanistan.
The identity of the other woman and her connection with Broadwell were not immediately known.
Petraeus has been married for 38 years to Holly Petraeus, the daughter of the West Point superintendent when he was a student at the New York school.
Concerned that the emails he exchanged with Broadwell raised the possibility of a security breach, the FBI brought the matter up with Petraeus directly, according to the official, who spoke on condition of anonymity because he was not authorized to publicly discuss the investigation. The FBI approached the CIA director because his emails in the matter were in most instances sent from a personal account, not his CIA one.
Petraeus decided to quit, abruptly ending a high-profile career that might high culminated with a run for the presidency, a notion he was believed considering.
"Such behavior is unacceptable, both as a husband and as the leader of an organization such as ours," Petraeus wrote his staff.
Petraeus handed his resignation letter to President Barack Obama on Thursday, stunning many in the White House, the CIA and Congress. The news broke in the media before the House and Senate intelligence committees were briefed, officials say.
By Friday evening, multiple officials identified Broadwell, who spent the better part of a year reporting on Petraeus' time in Afghanistan.
Her best-selling biography, "All In: The Education of General David Petraeus," was written with Vernon Loeb, a Washington Post editor, and published in January. Since Petraeus's resignation on Friday, the book jumped from a ranking on Amazon of 76,792 on Friday to 111 by mid-Saturday.
The CIA was not commenting on the identity of the woman with whom Petraeus was involved.
Broadwell, who is married with two young sons, has not responded to multiple emails and phone messages. Broadwell planned to celebrate her 40th birthday party in Washington this weekend, with many reporters invited. But her husband emailed guests to cancel the event late Friday.
CIA officers long had expressed concern about Broadwell's unprecedented access to the director. She frequently visited the spy agency's headquarters in Langley, Va., to meet Petraeus in his office, accompanied him on his punishing morning runs around the CIA grounds and often attended public functions as his guest, according to two former intelligence officials.
As a military intelligence officer in the Army Reserve, Broadwell had a high security clearance, which she mentioned at public events as one of the reasons she was well suited to write Petraeus's story.
But her access was unsettling to members of the secretive and compartmentalized intelligence agency, where husbands and wives often work in different divisions, but share nothing with each other when they come home because they don't "need to know."
In one incident that caught CIA staff by surprise, Broadwell posted a photograph on her Facebook page of Petraeus with actress Angelina Jolie, taken in his 7th floor office where only the official CIA photographer is permitted to take photos. Petraeus had apparently given Broadwell the photo just hours after it was taken.
Petraeus' staff in Afghanistan similarly had been concerned about the time Broadwell spent with their boss on her multiple reporting visits to the war zone. Following standard military procedure with senior officers, they always had another staffer present when she met with him at his headquarters. Military officers close to him insist the affair did not begin when he was in uniform.
In the preface to her book, Broadwell said she first met Petraeus in the spring of 2006. She was a graduate student at the Kennedy School of Government at Harvard; he was visiting the university to discuss his experiences in Iraq and a new counterinsurgency manual he was working on.
She had graduated from West Point with academic, fitness, and leadership honors, according to a biography posted on her publisher's website that lists authors available for speaking engagements.
Harvard invited some students to meet with Petraeus, and Broadwell was among them because of her military background, which she wrote included being recalled to active duty three times to work on counterterrorism issues after the Sept. 11 attacks.
After Obama put Petraeus in charge in Afghanistan in 2010, Broadwell decided to expand her research into an authorized biography.
Broadwell has deep ties and friendships throughout the Washington media sphere and often was sought for comment on Petraeus' viewpoints as he proved harder and harder to reach.
The CIA director had lowered his media profile, stopping his practice of emailing reporters and ending once-common background interviews by the agency. That was especially the case after GOP allegations last spring that the Obama administration was leaking sensitive material to burnish its foreign policy reputation ahead of the presidential election, after a series of stories appeared about top secret operations aimed at al-Qaida in Yemen, and Iran's nuclear program. A White House-ordered investigation of those leaks continues.
Petreaus's resignation comes just before a crucial scheduled appearance before congressional intelligence committees next week to testify on what the CIA knew, and what it told the White House, before, during and after the attacks that killed the U.S. ambassador and three other Americans in Libya on Sept. 11.
Congressional officials say Petraeus' deputy, Michael Morell, will testify instead, as acting director of the CIA.
(Copyright 2012 by The Associated Press. All Rights Reserved.)