(WASHINGTON) -- Gen. John Allen, the 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 currently 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 written statement released Tuesday while en route to Perth, Australia. Panetta says he ordered the Pentagon Inspector General to investigate Allen on Monday.
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 relevant facts are determined. Panetta said that while the matter is being investigated by the Defense Department Inspector General, Allen will remain in his post as commander of the International Security Assistance Force, based in Kabul, Afghanistan.
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 Gen. 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 last Friday, citing the affair as his reason for stepping down from his post.
FBI agents were at the Broadwell 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, according to the sources.
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.
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.
Copyright 2012 ABC News Radio