General David Petraeus takes the oath of office as director of the CIA as his wife Holly looks on in September, 2011/AFP
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 20,000 to 30,000 pages of correspondence – mostly emails – between 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, a Petraeus family friend, had alerted the FBI earlier this year that she was receiving threatening anonymous emails, which were eventually traced back 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.
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