Washington, Nov 14 (IANS): The top US commander in Afghanistan is being probed for alleged "inappropriate" communications with a woman linked to the Petraeus scandal.

US Defence Secretary Leon Panetta said Tuesday that he has ordered to open a probe of General John Allen after the FBI referred a matter involving him to the Pentagon Sunday.

Allen will remain commander of the International Security Assistance Force (ISAF) while the case is under investigation, Xinhua quoted Panetta as saying.

The FBI has uncovered thousands of alleged "potential inappropriate" emails between Allen and Jill Kelly, a central figure in Petraeus' scandal.

CIA Director David Petraeus resigned last Friday after confessing to an extramarital relationship.

FBI began probing 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.

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

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.

Allen became the ISAF commander and commander of US forces in Afghanistan in July 2011.

US lawmakers on both sides have criticised the Federal Bureau of Investigation (FBI) for not notifying the Congressional intelligence and security panels of the probe into Petraeus's scandal.