The Pentagon is investigating allegations that the woman whose complaint led to the resignation of CIA Director David Petraeus received "inappropriate communications" from the man who replaced him as the Allies' senior commander in Afghanistan.
It has reported that the FBI has discovered up to 30,000 pages of suspect e-mails between Gen John R. Allen, commander of US and NATO troops in Afghanistan, and Jill Kelley, who triggered the resignation of Petraeus by contacting the Bureau to report threatening e-mails from Paula Broadwell.
It subsequently emerged that Patraeus and Broadwell were having an affair, prompting Petraeus to resign on 9 November.
Defence Secretary Leon Panetta told reporters that he ordered the investigation into the Allen-Kelley e-mail chain, as the FBI had referred the matter to the Pentagon. Officials are now investigating the nature of the e-mails on lines of explicit content or any leak of classified documents.
Panetta has also put Allen's nomination to be Nato's Supreme Allied Commander in Europe on hold "until the relevant facts are determined," a decision with which President Barack Obama reportedly concurs.
However Allen, who is a four-star Marine general, is expected to retain his command of Allied troops in Kabul. He succeeded Petraeus as the top US commander in Afghanistan in July 2011.
The probe came ahead of Allen's appearance before a Senate hearing to confirm his appointment as Nato's head in Europe.
"Gen Allen disputes that he has engaged in any wrongdoing in this matter," a senior official told the Los Angeles Times on condition of anonymity.
Meanwhile, FBI officials are searching the home of Paula Broadwell. Agents arrived at her property carrying briefcases, plastic tubs and cardboard boxes, shortly before 21:00 local time (02:00 GMT). It was not clear whether Broadwell or any of her family members were at the home.
Though the FBI spokeswoman in Charlotte, Shelley Lynch confirmed the search, she did not divulge further details.