Updated 8:48 am.

The sex scandal that brought down former Army general and CIA Director David Petraeus has expanded to engulf another senior official: Marine Corps Gen. John Allen, the commander of U.S. and NATO troops in Afghanistan.

Allen, who is married, allegedly exchanged what’s being described as “inappropriate communication” with Jill Kelley, the 37-year-old Tampa socialite who claims she received threatening emails from Petraeus’ mistress (and biographer) Paula Broadwell. Kelley reportedly approached the FBI with the alleged threats, kicking off the investigation that ultimately uncovered Petraeus’ affair with Broadwell and prompted the retired four-star general to resign from the CIA last week.

The news of Allen’s alleged involvement in l’affair de Petraeus broke early Tuesday morning when Defense Secretary Leon Panetta, en route to Australia, released a statement to reporters traveling with him. Panetta said the FBI told him on Sunday that it was investigating Allen, who succeeded Petraeus as head of the International Security Assistance Force in Afghanistan in July 2011 and has overseen the beginning of the America’s staged withdrawal from the conflict.

Panetta immediately notified the White House, the Congressional armed services committees and the Defense Department Inspector General of the Allen probe, according to The Washington Post.

Allen’s former aides in Kabul can’t believe that their former boss has been entangled in this tawdry mess. “The Gen. Allen that I worked for is a man who is very serious about the public trust,” Lt. Col. Ray Kimball, an Army officer who served on Allen’s staff for nearly a year, tells Danger Room. “I never heard the name Jill Kelley until this weekend.”

Allen was expected to hand over command of the Afghanistan war to Marine Gen. Joseph Dunford in coming weeks. The plan was that Allen would then take over as military head of NATO and U.S. European Command. Panetta has reportedly moved up Dunford’s ascension and put Allen’s European posting on ice, according to The New York Times. Allen is reportedly in Washington as of Tuesday.

“I have asked the President – and the President has agreed – to put his nomination on hold until the relevant facts are determined,” Panetta said in a statement.

“While the matter is under investigation and before the facts are determined, General Allen will remain commander of ISAF,” Panetta added. “His leadership has been instrumental in achieving the significant progress that ISAF, working alongside our Afghan partners, has made in bringing greater security to the Afghan people and in ensuring that Afghanistan never again becomes a safe haven for terrorists. He is entitled to due process in this matter.”

It’s not clear from initial reports what exactly “inappropriate communication” means. (Allen, for his part, “disputes that he has engaged in any wrongdoing in this matter,” according to an unnamed senior defense official.)

“He’s never been alone with her,” another unnamed official tells the Washington Post. “Did he have an affair? No.”

Allen and Kelley did exchange “a few hundred emails over a couple of years,” the official added. But “most of them were about routine stuff.”

“I don’t even know what he’s supposedly being accused of, and I don’t think anyone else outside of the DODIG [Department of Defense Inspector General] does either,” says Kimball.

“The FBI’s decision to refer the Allen matter to the Pentagon rather than keep it itself, combined with Panetta’s decision to allow Allen to continue as Afghanistan commander without a suspension, suggested strongly that officials viewed whatever happened as a possible infraction of military rules rather than a violation of federal criminal law,” notes the Associated Press’ veteran Pentagon correspondent Bob Burns.

Kelley, who is married, is a volunteer “social liaison” to MacDill Air Force Base in Tampa, home to U.S. Central Command and Special Operations Command, both deeply involved in the Afghanistan war. She is said to have hosted parties for military personnel at her million-dollar home.

Broadwell apparently perceived Kelley as some sort of threat to Broadwell’s relationship with Petraeus. Media reports have portrayed Kelley and her husband as close friends of Petraeus and his wife of 37 years.

Both Broadwell and Kelley are doing their best to escape the intensifying media spotlight. Petraeus, for his part, has not made any public statement since his surprise resignation on Friday. (Although some of his former aides are speaking out.) It’s unclear whether Petraeus, who has been temporarily succeeded at the CIA by his former deputy Michael Morell, will testify as planned in the ongoing Congressional investigation into the September attack on the U.S. consulate in Benghazi, Libya.

Regardless of the outcome of the FBI investigation of Allen’s communications, the probe comes at a critical time for the U.S.-led war effort in Afghanistan. Insider attacks continue as U.S. and NATO forces struggle to train up enough Afghan forces to replace the main foreign force that’s scheduled to withdraw in 2014. The U.S. is expected to maintain a smaller advisory force, though how big and for how long have yet to be announced.

Whatever Allen did to become entangled in the Petraeus-Broadwell-Kelley scandal, it’s certainly an unwelcome distraction from the hard work of winding down a painful, 11-year-old war.