Nov. 13, 2012— -- President Obama is backing Gen. John Allen, the commander of American forces in Afghanistan and the second top military official whose behavior with a woman has come under investigation in recent weeks.
Allen, a four-star Marine general, is being investigated by the Pentagon's inspector general for "potentially inappropriate" emails with Florida socialite Jill Kelley.
The probe into Allen emerged from an FBI investigation into former CIA Director David Petraeus -- Allen's predecessor in Afghanistan -- who resigned and admitted having an extramarital affair. Petraeus' alleged mistress has been identified as the author of his biography Paula Broadwell.
While Obama accepted Petraeus' resignation last week, the president continues to have "faith" in Allen, White House Press Secretary Jay Carney said today.
"I can tell you that the president thinks very highly of General Allen and his service to his country, as well as the job he has done in Afghanistan," Carney said of the commander of the International Security Assistance Force in Afghanistan.
Allen had been nominated as the next commander of U.S. European Command and the commander of NATO forces in Europe, and despite Obama's backing, the nomination has been put on hold. The change of command at NATO is currently slated to not take place until March at the earliest.
A Defense Department official said the probe into Allen includes a review of 20,000 to 30,000 emails between the general and Kelley, including some characterized as "inappropriate" and "flirtatious."
Allen denies he was involved in an affair, the Pentagon official said. An intermediary for the general told ABC News that Allen and his wife are friends with Kelley and her husband and most of the emails were sent from Kelley to Allen's wife.
The source said Allen and Kelley would correspond frequently by email, as much as 11 times a day, but that the emails were "innocuous." The source insisted there was no sex between Allen and Kelley.
A U.S. official said Allen may have triggered the investigation when he got an anonymous email a few months ago that was traced to Broadwell. The email had a "Kelley Patrol" return address or subject line and painted Kelley as a seductress, which Allen found alarming and mentioned to Kelley in a subsequent email, the official said.
The official described Kelley, who had been given the title as honorary ambassador to the Central Command, as a "nice, bored rich socialite who drops the honorary from her title..and tells people she is an ambassador. She gets herself in anything related to Centcom and all the senior people and has been for years."
See the timeline of the Petraeus/Broadwell affair HERE.
Secretary of Defense Leon 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. A Defense Department official says Panetta has not spoken to Allen in that time frame.
The official says the FBI provided the emails to DOD because they were not within their jurisdiction, and that they could fall under the Uniform Code of Military Justice, a set of guidelines that is applicable to all members of the U.S. military at home and abroad.
Read what top Senators are saying about the Petraeus affair HERE.
Allen was supposed to appear before a Senate confirmation hearing this Thursday alongside his designated replacement, Marine Gen. Joseph Dunford.
Panetta said 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 allegedly 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 an 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.
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.
As the details of the investigation launched by the FBI unraveled this weekend, Kelley's name emerged.
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, officials have said. The FBI traced the messages to Broadwell's computer, where they found what one official described as 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' Sarah Parnass and the Associated Press contributed to this report.