In a statement released to reporters on his plane en route to Australia early Tuesday, Defence Secretary Leon E. Panetta said that the FBI had informed him on Sunday of its investigation of Allen.
Panetta turned the matter over to the Pentagon's inspector general to conduct its own investigation into what the defence official said were 20,000 to 30,000 pages of documents, many of them emails between Allen and Kelley, who is married with children and lives in Tampa, Florida.
Asked if the FBI had determined that there was criminal action involved, the defence official replied, "That is for the FBI to discuss."
The official, who briefed reporters on Panetta's plane, said that "there is the distinct possibility" that the emails were connected to an ongoing FBI investigation into Petraeus and Broadwell.
The defence official said that Allen, who is also married, told Pentagon officials he had done nothing wrong. Panetta's statement praised Allen for his leadership in Afghanistan and said that "he is entitled to due process in this matter."
But the two investigations open what could be widening scandal into two of the most prominent generals of their generation - Petraeus, who was the top commander in Iraq and Afghanistan before he retired from the military and became director of the CIA, only to resign Friday because of the affair, and Allen, who also served in Iraq and now commands 68,000 U.S. troops in Afghanistan.
Although Allen will remain the commander in Afghanistan, Panetta said that he had asked President Barack Obama to put on hold Allen's nomination to be the commander of U.S. forces in Europe and the Supreme Allied Commander of NATO, two positions he was to move into after what was expected to be easy confirmation by the Senate. Panetta said in his statement that Obama agreed with his decision.
Gen. Joseph A. Dunford, the assistant commandant of the Marine Corps who was nominated last month by Obama to succeed Allen in Afghanistan, will proceed as planned with his confirmation hearing. In his statement, Panetta urged the Senate to act promptly on his nomination.
The defence official said that the emails between Kelley and Allen spanned the years 2010 to 2012. The official could not explain why there were so many pages of emails and did not specify their content. The official said he could not explain how the emails between Kelley and Allen were related to the emails between Petraeus and Broadwell and emails between Broadwell and Kelley.
In what is known so far, Kelley went to the FBI last summer after she was disturbed by harassing emails. The FBI began an investigation and learned that the emails were from Broadwell. In the course of looking into Broadwell's emails, the FBI discovered emails between Broadwell and Petraeus that indicated they were having an extramarital affair. Broadwell, officials say, saw Kelley as a rival for her affections with Petraeus.
The defence official said he did not know how Allen and Kelley knew each other. Allen has been in Afghanistan as the top U.S. commander since July 2011, although before that he lived in Tampa as the deputy commander for Central Command, which oversees U.S. military operations in the Middle East.
The defence official said that the Pentagon had received the 20,000 to 30,000 pages of documents from the FBI and was reviewing them.
The defence official said that at 5 p.m. Washington time on Sunday, Panetta was informed by the Pentagon's general counsel of the FBI investigation into Kelley. Panetta was at the time on his plane en route from San Francisco to Honolulu, his first stop on a weeklong trip to the Pacific and Asia. Panetta notified the White House and then the leaders of the Senate and House Armed Services Committee.
Allen is in Washington for what was to be his confirmation hearing as commander in Europe. That hearing, the official said, will be delayed.