WASHINGTON - The top US commander in Afghanistan has been put under investigation for alleged "inappropriate" communications with a woman involved in the scandal that forced out CIA Director David Petraeus.

US Defense Secretary Leon Panetta said Tuesday that he has directed the inspector general of the department to open an investigation of General John Allen after the FBI referred a matter involving him to the Pentagon on Sunday.

USMC Lt. General John Allen (L) and US Army General David Petraeus (C) greet US Secretary of Defense Leon Panetta after Panetta's arrival in Kabul, Afghanistan in this July 9, 2011 file photograph. [Photo/Agencies]

Allen will remain commander of the International Security Assistance Force (ISAF) while the case is under investigation, said Panetta, adding that the case should also be notified to the US Senate Armed Services Committee.

Allen became the ISAF commander and commander of US forces in Afghanistan in July 2011. His nomination to be the next commander of US European Command and the commander of NATO forces in Europe is put on hold until relevant facts are determined.

Panetta has also asked the ranking members of the Senate Armed Services Committee to delay the scheduled confirmation hearing on Allen's pending nomination.

"Obviously, it was a very sad situation, to have a distinguished career like that end in this manner," said Panetta on Monday en route to Perth, Australia, referring to the resignation of Petraeus.

ABC news quoted a senior defense official as saying that the FBI has uncovered thousands of alleged "potential inappropriate" emails between Allen and Jill Kelly, a central figure in Petraeus' scandal.

Petraeus's announcement of resignation last Friday after confessing to an extramarital relationship shocked Washington.

Media reports over the weekend said that the FBI began investigating the case after Kelly, a friend of the Petraeus family, complained to law enforcement about receiving anonymous and threatening emails. The FBI traced the emails to Paula Broadwell, Petraeus's biographer, and then discovered that Broadwell was Petraeus' girlfriend.

Petraeus, a retired four-star general who served more than 37 years in the US Army, took the office as the director of CIA in September, 2011. He had overseen all coalition forces in Iraq and led the military campaign in Afghanistan.

US lawmakers on both sides have criticized the FBI for not notifying the Congressional intelligence and security panels of the probe into Petraeus's scandal.

Democratic Senator Dianne Feinstein, chairwoman of the Senate Intelligence Committee, said on Monday that her concern about the case had escalated over the last few days as more details popped up.

The panel, she said, will investigate why the FBI failed to alert the panel immediately about Petraeus's scandal.