Sources told CBS News the emails were never actually transmitted, a ruse used by teenagers, terrorists and others who want to communicate electronically without the risk of being hacked. The FBI began the investigation because of the possibility Broadwell herself had hacked Petraeus' email.
The FBI investigation that led to Petraeus' resignation now includes U.S. Marine Corps Gen. John R. Allen, the Pentagon said Tuesday.
At the same time, an FBI agent investigating Petraeus' extramarital affair was banned from the probe after he allegedly sent shirtless photos of himself to Jill Kelley, a 37-year-old Tampa, Fla., woman whose close friendship with Petraeus is tied to his downfall, The Wall Street Journal reported.
FBI officials were to brief the Senate and House intelligence committees about the case Tuesday.
Concerning Allen, the FBI uncovered 20,000 to 30,000 pages of "potentially inappropriate" emails between the four-star general and Kelley, a senior defense official told The Washington Post.
Kelley reportedly received threatening emails from Paula Broadwell, the woman with whom Petraeus had an extramarital affair.
FBI agents searched Broadwell's home in Charlotte, N.C., Monday and were seen by reporters carrying away boxes. A law enforcement official told The New York Times Broadwell had consented to the search.
Allen succeeded Petraeus as commander of U.S. and NATO troops in Afghanistan in July. He since was appointed NATO's supreme allied commander for Europe and is scheduled to take office in early 2013, pending Senate confirmation originally set to begin Thursday.
The nomination is now on hold "until the relevant facts are determined," Defense Secretary Leon Panetta said.
Allen, in Washington preparing for the hearings, had no immediate comment. He also had no advance warning of the investigation, learning of it from Joint Chiefs of Staff Chairman Gen. Martin Dempsey Monday night, a close Allen aide told NBC News.
The FBI first told the Pentagon of its investigation into Allen's communications with Kelley Sunday, Panetta said in a statement on a flight from Honolulu to Perth, Australia, early Tuesday.
In the statement, Panetta said the FBI referred "a matter involving" Allen to the Pentagon.
Panetta said he referred the investigation into Allen and the emails to the Defense Department's inspector general Monday.
Asked if the FBI determined whether any action was criminal, a defense official said, "That is for the FBI to discuss," The New York Times reported.
The official, who briefed reporters en route to Australia, said "there is the distinct possibility" that the emails were linked to an FBI investigation into Petraeus and Broadwell.
Panetta's statement also praised Allen for his leadership and said the general was "entitled to due process in this matter."
Meanwhile, an FBI agent who triggered the Petraeus investigation was barred over the summer from participating in the case after the bureau discovered he allegedly sent shirtless photos of himself to Kelley before the investigation began, the Journal said.
The unidentified agent, a friend of Kelley, now is being investigated by the FBI's internal affairs Office of Professional Responsibility, two officials familiar with the matter told the Journal.
Kelley complained in May about receiving threatening emails to the agent, who referred the case to a cyber crimes unit, which opened an investigation, the Journal said.
Although Allen will remain commander in Afghanistan, Panetta said President Obama agreed to a request to put on hold Allen's nomination to be commander of U.S. forces in Europe and the Supreme Allied Commander of NATO, the Times said.
The Senate confirmation hearing for Gen. Joseph Dunford, the Marine Corps assistant commander Obama nominated to succeed Allen in Afghanistan, will proceed as planned, the Times said. In his statement, Panetta urged the Senate to act promptly.
White House Press Secretary Jay Carney, speaking at a news conference Tuesday, said President Obama "thinks very highly of General Allen and his service to his country, as well as the job he has done in Afghanistan," and reiterated the delay in Allen's nomination is at the request of Panetta.