PERTH, Australia — Gen. John Allen, the top American and NATO commander in Afghanistan, has become ensnared in the scandal over an extramarital affair acknowledged by David H. Petreaus, a former general. General Allen is being investigated for what a senior defense official said early Tuesday was “inappropriate communication” with Jill Kelley, the woman in Tampa, Fla., who was seen by General Petreaus’s former lover as a rival for his attentions.
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.
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.”
But 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.
The defense official said that the e-mails between Ms. Kelley and General Allen spanned the years 2010 to 2012. The official could not explain why there were so many pages of e-mails and did not specify their content. The official said he could not explain how the e-mails between Ms. Kelley and General Allen were related to the e-mails between Mr. Petraeus and Ms. Broadwell and e-mails between Ms. Broadwell and Ms. Kelley.
In what is known so far, Ms. Kelley went to the F.B.I. last summer after she was disturbed by harassing e-mails. The F.B.I. began an investigation and learned that the e-mails were from Ms. Broadwell. In the course of looking into Ms. Broadwell’s e-mails, the F.B.I. discovered e-mails between Ms. Broadwell and Mr. Petraeus that indicated they were having an extramarital affair. Ms. Broadwell, officials say, saw Ms. Kelley as a rival for her affections with Mr. Petraeus.
The defense official said he did not know how General Allen and Ms. Kelley knew each other. General Allen has been in Afghanistan as the top American commander since July 2011, although before that he lived in Tampa as the deputy commander for Central Command, which oversees American military operations in the Middle East.
The defense official said that the Pentagon had received the 20,000 to 30,000 pages of documents from the F.B.I. and was currently reviewing them.
The defense official said that at 5 p.m. Washington time on Sunday Mr. Panetta was informed by the Pentagon’s general counsel that the F.B.I. had the thousands of pages of e-mails between General Allen and Ms. Kelley. Mr. 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. Mr. Panetta notified the White House and then the leaders of the Senate and House armed services committees.
General Allen is now in Washington for what was to be his confirmation hearing as commander in Europe. That hearing, the official said, will now be delayed.
After arriving in Perth Mr. Panetta and Secretary of State Hillary Rodham Clinton met with Prime Minister Julia Gillard of Australia for a United States-Australian security and diplomatic conference. Asked by a reporter while pausing for photos with Mrs. Clinton and Ms. Gillard if General Allen could remain an effective commander while under investigation, Mr. Panetta said nothing.
Gen. Martin E. Dempsey, the chairman of the Joint Chiefs of Staff, was also in Perth for the defense meetings and had no comment on the investigation of General Allen. "I do know him well and I can’t say," General Dempsey said of General Allen late on Tuesday after returning from an official dinner with the Australian officials, Mrs. Clinton and Mr. Panetta.
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Top U.S. Commander in Afghanistan Is Linked to Petraeus Scandal
