Gen. John Allen, a married father and a four-star Marine general, is being investigated by the FBI for tens of thousands of possibly inappropriate emails to 37-year-old Jill Kelley, the woman at the center of Petraeus' sex scandal. The email exchanges took place from 2010 to 2012.
Kelley is a Petraeus family friend who alerted the FBI after she allegedly received threatening emails. Those messages were traced back to Petraeus' mistress and biographer, Paula Broadwell. The affair forced Petraeus to resign as head of the CIA on Friday.
A senior defense official said the emails between Allen and Kelley were "flirtatious," but it was unclear whether Allen was flirting, or if he was the recipient of the flirting.
President Barack Obama has backed Allen. White House Press Secretary Jay Carney said the president "thinks very highly of General Allen and his service to his country, as well as the job he has done in Afghanistan."
Allen had been nominated to become the next commander of U.S. European Command and the commander of NATO forces in Europe, but the appointment has been put on hold at Defense Secretary Leon Panetta's request. Instead, Allen could face charges of adultery, which is a crime under the Uniform Code of Military Justice. Allen has denied wrongdoing.
Before Kelley's name was linked to Allen, her brother, David Khawam, defended her to reporters on Monday.
"She's very dedicated to her husband and to her kids," he said. "Something like this is really pretty much a fluke. So for anybody to paint her other than that, it's completely wrong."
Kelly was apparently so close to Petraeus and Allen that she persuaded both to write letters on behalf of her twin sister in a custody battle.
Overnight, nearly a dozen federal agents searched Broadwell's North Carolina home. They left with a desktop computer, cardboard boxes and a briefcase.
The FBI says she and Petraeus exchanged thousands of emails, many salacious in nature. They believe she sent Kelley threatening emails because she was jealous of her.
Extramarital affairs are viewed as particularly risky for intelligence officers because they might be blackmailed to keep the affair quiet.
Later Tuesday, the Senate Intelligence Committee, headed by California Rep. Dianne Feinstein, met to discuss how the investigation was handled by the FBI, which was been criticized for not notifying the White House of their probe earlier. The FBI is now putting together a timeline of their investigation.
According to ABC News, Petraeus traveled to Libya late October to conduct his own review of the Benghazi attack that killed four Americans and was planning to testify before Congress. But Petraeus chose not to testify Tuesday, saying acting CIA Director Michael Morell is in possession of all the information Petraeus gathered - and if he did testify, it would be a media circus. Morell ended up testifying in a closed-door session.
The Washington Post reports the FBI is making a new push to figure out how Petraeus' mistress obtained classified material and whether that material actually came from Petraeus.
ABC News and The Associated Press contributed to this report.