The revelation represented yet another stunning turn in a widening scandal that has jolted Washington only days after the re-election of President Barack Obama, with lawmakers vowing to get to the bottom of case.
The Pentagon official told reporters the FBI had uncovered a trove of 30 000 pages of correspondence – mostly emails – between General John Allen and Jill Kelley, a key figure in the scandal that brought down the CIA chief.
Petraeus – a former four-star general who had previously led the US wars in Iraq and Afghanistan – resigned abruptly last week over an extramarital affair with his biographer Paula Broadwell.
Kelley, of Tampa, Florida, had alerted the FBI to receiving threatening emails earlier this year that were eventually traced to Broadwell. The FBI then found emails between Broadwell and Petraeus that revealed their affair.
The senior US defence official, speaking on condition of anonymity, told reporters travelling with Defence Secretary Leon Panetta there was a "distinct possibility" the Allen emails were connected to the Petraeus investigation.
"The allegations involve inappropriate communications" between Allen and Kelley, the official said.
Panetta said in a statement that his department was informed by the FBI on Sunday about the case and that he had referred it to the Pentagon's inspector general for investigation.
He said Allen would remain in Kabul as the commander of Nato-led security forces but that he had asked the Senate Armed Services Committee to delay action on Allen's pending nomination to be Nato's supreme allied commander.
Panetta praised the general's work in Afghanistan, saying his leadership has been "instrumental" in securing progress in the war against Taliban insurgents.
However, Panetta said he requested the Senate committee move promptly on the nomination for Allen's successor in Afghanistan, General Joseph Dunford.
It remained unclear what allegations Allen faced, and officials declined to comment on whether the Marine general was accused of using his work email to communicate with Kelley or had disclosed any classified information.
"It's far too early to speculate on what the IG [inspector general] might find," the same defence official said.
"There is enough concern that we believe it was a prudent measure to take appropriate steps to direct an investigation and notify Congress," he said.
"We need to see where the facts lead in this matter, before jumping to any conclusions whatsoever."
He added that Allen "disputes that he has engaged in any wrongdoing in this matter."
Kelley, a 37-year-old Tampa socialite with close military ties, was a family friend of the Petraeuses.
Both Petraeus and Allen served in Tampa, home to US Central Command, which Petraeus led before taking over as commander in Afghanistan in 2010. – Sapa-AFP