PERTH, Australia — Gen. John R. Allen, the top American and NATO commander in Afghanistan, has become ensnared in the scandal over an extramarital affair acknowledged by David H. Petraeus, a former general. General Allen is being investigated for what a senior defense official said early Tuesday was “inappropriate communication” with Jill Kelley, a woman in Tampa, Fla., who was seen by Mr. Petraeus’s lover as a rival for his attentions.
Chuck Burton/Associated Press
F.B.I. agents carried boxes and a computer from the home of Paula Broadwell on Tuesday.
In a statement released to reporters on his plane en route to Australia early Tuesday, Defense Secretary Leon E. Panetta said that the F.B.I. on Sunday had referred “a matter involving” General Allen to the Pentagon.
Mr. Panetta turned the matter over to the Pentagon’s inspector general to conduct an investigation into what a defense official said were 20,000 to 30,000 pages of documents, many of them e-mails between General Allen and Ms. Kelley, who is married and has children.
A senior law enforcement official in Washington said on Tuesday that F.B.I. investigators, looking into Ms. Kelley’s complaint about anonymous e-mails she had received, examined all of her e-mails as a routine step.
“When you get involved in a cybercase like this, you have to look at everything,” the official said, suggesting that Ms. Kelley may not have considered that possibility when she filed the complaint. “The real question is why someone decided to open this can of worms.”
The official would not describe the content of the e-mails between General Allen and Ms. Kelley or say specifically why F.B.I. officials decided to pass them on to the Defense Department. “Generally, the nature of the e-mails warranted providing them to D.O.D.,” he said.
Under military law, adultery can be a crime.
The defense official on Mr. Panetta’s plane said that General Allen, who is also married, told Pentagon officials he had done nothing wrong. Neither he nor Ms. Kelley could be reached for comment early Tuesday. Mr. Panetta’s statement praised General Allen for his leadership in Afghanistan and said that “he is entitled to due process in this matter.”
A senior Defense Department official said General Allen has denied having an extramarital affair with Ms. Kelley. But the official said the content of some of the e-mails “was of a flirtatious nature; some were of an affectionate nature.”
“That is what makes the e-mails potentially inappropriate,” the official said, adding that it was unclear whether the tone of flirtation was from General Allen to Ms. Kelley or from Ms. Kelley to General Allen, or both.
The official said he had not read the e-mails but had been briefed on the content, and he said that they did not contain anything inappropriate regarding operations or security. Pentagon officials cautioned against making too much of the number of documents, since some might be from e-mail chains, or brief messages printed out on a whole page, or simply copies of messages sent to other people.
The Pentagon inspector general’s investigation opens up what could be a widening scandal into two of the most prominent generals of their generation: Mr. Petraeus, who was the top commander in Iraq and Afghanistan before he retired from the military and became director of the C.I.A., only to resign on Friday because of the affair, and General Allen, who also served in Iraq and now commands 68,000 American troops in Afghanistan.
Although General Allen will remain the commander in Afghanistan, Mr. Panetta said that he had asked President Obama to delay the general’s nomination to be the commander of American 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. Mr. Panetta said in his statement that Mr. Obama agreed with his request.
Gen. Joseph A. Dunford, the assistant commandant of the Marine Corps who was nominated last month by Mr. Obama to succeed General Allen in Afghanistan, will proceed as planned with his confirmation hearing. In his statement, Mr. Panetta urged the Senate to act promptly on his nomination.
The National Security Council spokesman, Tommy Vietor, said in a statement on Tuesday that Mr. Obama also believes that the Senate should swiftly confirm General Dunford.
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