Gen. John Allen, commander of the International Security Assistance Force in Afghanistan, is under investigation for alleged "inappropriate communications" with Jill Kelley, the woman who is said to have received threatening emails from Paula Broadwell, the woman with whom former CIA Director David Petraeus had an extramarital affair.
The FBI has uncovered "potentially inappropriate" emails between Allen and Kelly, according to a senior U.S. defense official who is traveling with Defense Secretary Leon Panetta. The department is reviewing between 20,000 and 30,000 documents connected to this matter, the official said. The email exchanges between Kelley and Allen took place from 2010 to 2012.
Panetta says the FBI referred the matter to the Pentagon on Sunday, according to a statement he released Tuesday while en route to Perth, Australia. Panetta says he ordered the Pentagon inspector general to investigate Allen on Monday.
See the timeline of the entire Petraeus/Broadwell affair HERE.
Allen disputes that he has engaged in any wrongdoing in this matter, according to the official.
Allen, a four-star Marine general, succeeded Petraeus as the top American commander in Afghanistan in July 2011.
In the meantime, Panetta said, Allen's nomination to be the next commander of U.S. European Command and the commander of NATO forces in Europe has been put on hold "until the relevant facts are determined." He had been expected to take that new post in early 2013, if confirmed by the Senate, as had been widely expected.
Allen was supposed to appear before a Senate confirmation hearing this Thursday alongside his designated replacement, Marine Gen. Joseph Dunford. Panetta has asked the Senate Armed Services Committee hearing to delay Allen's hearing, but proceed with Dunford's nomination.
Panetta said President Obama has agreed to put Allen's nomination on hold until the facts are determined. Panetta said that while the matter is being investigated by the Defense Department IG, Allen will remain in his post as commander of the International Security Assistance Force, based in Kabul.
The senior Defense official said, "We'll have to let the process follow its course. As I said, and you'll see in the Secretary's statement, we believe that General Allen is entitled to due process. We need to see where the facts lead in this matter before jumping to any conclusions whatsoever."
The official added, "We're in the very early stages of reviewing the documents right now. This matter has been referred to the IG, the IG will do a thorough investigation of the documents."
Kelley is said to have received threatening emails from Broadwell, who is Petraeus' biographer and who had an extramarital affair with Petraeus that reportedly began two months after he became CIA director in September 2011.
Petraeus resigned as CIA director on Friday citing the affair as his reason for stepping down from his post.
FBI agents spent more than four hours at Broadwell's home in North Carolina Monday night to carry out a consensual search that had been arranged with her lawyers, law enforcement sources said. The search was to locate additional classified material on computers or documents in the home, the sources said.
Agents left the house with a desktop computer, cardboard boxes and a briefcase. They walked through the open garage of Broadwell's house and knocked at a side door before entering the home. One person was taking photographs of the house and its garage as members of the news media watched.
Broadwell appears to be cooperating with investigators in an effort to make this go away, to show that she has nothing else to hide, the sources said.
An assistant to Washington lawyer Robert F. Muse told ABC News that Muse is representing Broadwell. Muse works for the same firm as the lawyer who represented Monica Lewinsky.
The firm, Stein, Mitchell, Muse & Cipollone, boasts such high-profile clients as Lewinsky, former Sen. Bob Packwood, R-Ore., AFL-CIO officials and Ambassador Lewis Tambs in the Iran-Contra Investigation.
Petraeus could possibly face military prosecution for adultery if officials turn up any evidence to counter his apparent claims that the affair began after he left the military.
A friend of Petraeus, retired U.S. Army Col. Steve Boylan, told ABC News, that the affair began several months after his retirement from the Army in August 2011 and ended four months ago.
Broadwell, 40, had extraordinary access to the 60-year-old general during six trips she took to Afghanistan as his official biographer, a plum assignment for a novice writer.
The timeline of the relationship, according to Petraeus, would mean that he was carrying on the affair for the majority of his tenure at the CIA, where he began as director Sept. 6, 2011. If he carried on the affair while serving in the Army, however, Petraeus could face charges, according to Article 134 of the Uniform Code of Military Justice, which reprimands conduct "of a nature to bring discredit upon the armed forces."
As the details of the investigation launched by the FBI unraveled this weekend, it became clear that the woman at the heart of the inquiry that led to Petraeus' downfall had been identified as Jill Kelley, a Florida woman who volunteers to help the military. She is a family friend of Petraeus, who Broadwell apparently felt threatened by.
Kelley and her husband are longtime supporters of the military, and six months ago she was named "Honorary Ambassador to Central Command" for her volunteer work with the military. Officials say Kelley is not romantically linked to Petraeus, but befriended the general and his wife when he was stationed in Florida. The Kelleys spent Christmases in group settings with the Petraeuses and visited them in Washington D.C., where Kelley's sister and her son live.
"We and our family have been friends with Gen. Petraeus and his family for over five years." Kelley said in a statement Sunday. "We respect his and his family's privacy and want the same for us and our three children."
Earlier this year, around the time that Petraeus and Broadwell were breaking off their affair, Kelley began receiving anonymous emails, which she found so threatening she went to authorities. The FBI traced the messages to Broadwell's computer, where they found other salacious and explicit emails between Broadwell and Petraeus that made it clear to officials that the two were carrying on an affair.
An official told ABC News the FBI uncovered "hundreds if not thousands of emails between Petraeus and Broadwell," many of them salacious in nature.
ABC News' Martha Raddatz, Sarah Parnass and the Associated Press contributed to this report.
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