Allen, a Marine, succeeded Petraeus as the top allied commander in Afghanistan in July 2011. He also served as Petraeus’s deputy when both generals led the military’s Tampa-based Central Command from 2008 until 2010.
The FBI first notified the Pentagon of its investigation into Allen’s communications with Kelley on Sunday evening, according to the senior defense official, who spoke on condition of anonymity to discuss details of the pending case.
In response, Pentagon chief Leon E. Panetta referred the investigation on Monday to the Defense Department’s Inspector General for further review, according to a statement released by Panetta early Tuesday as he was traveling to Australia.
The Pentagon did not address the nature of Kelley’s alleged relationship with Allen. But another senior U.S. official, who is close to Allen, strongly denied that the general and Kelley had an affair or engaged in inappropriate communication. Allen and Kelley, who threw parties and other social events involving senior leaders at the Central Command, did exchange “a few hundred e-mails over a couple of years,” beginning when Allen was the deputy commander at the Central Command, this senior official said. But “most of them were about routine stuff.”
“He’s never been alone with her,” the senior official said. “Did he have an affair? No.”
The senior official also emphasized that the volume of communications between the two “was nowhere near” 20,000 to 30,000 personal messages. The official said the high page count reported by the FBI may have been the result of printing numerous individual messages that contained lengthy threads of earlier exchanges.
The senior official said Allen received at least one e-mail about Kelley from an unidentified account that eventually was traced to Paula Broadwell, a former Army officer who was Petraeus’s biographer and, it turns out, his mistress.
Allen discussed that e-mail with Kelley, who was receiving a slew of harassing messages at the time, the senior official who is close to Allen said. Kelley, who did not know the messages were being sent by Broadwell, notified the FBI.
Some of the e-mails may have prompted suspicions among FBI investigators because Allen sometimes used words such as “sweetheart” to refer to her, the senior official said. But the official added that Allen, who was raised in Virginia, employed that language as a term of platonic friendship, not romantic interest.