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New York Times

President Barack Obama has faith in Gen. John R. Allen, the top U.S. and NATO commander in Afghanistan, the White House spokesman said Tuesday, after it was disclosed that the general was under investigation for what the Pentagon called "inappropriate communication" with the Tampa woman whose complaint to the FBI set off the scandal involving David Petraeus' extramarital affair.

"The president thinks very highly of Gen. Allen," White House spokesman Jay Carney said at a news briefing. "He has faith in Gen. Allen," and believes that he has done "an excellent job" as commander in Afghanistan, Carney added.

Obama put a hold Allen's nomination to become the next commander of U.S. European Command as well as the NATO supreme allied commander in Europe after investigators uncovered 20,000-plus pages of documents and emails that involved Allen and Jill Kelley of Tampa. Some of the material was characterized as "flirtatious."

Allen, 58, insisted he'd done nothing wrong and worked to save his imperiled career.

Panetta and other officials disclosed overnight the investigation into Allen's emails with Kelley, who was seen by Paula Broadwell, Petraeus' lover, as a rival.

Petraeus' affair led to his resignation as head of the CIA on Friday, and the FBI's investigations into emails in the matter apparently led in turn to Allen's correspondence.

In a statement released to reporters on his plane en route to Australia early Tuesday, Panetta said the FBI on Sunday had referred "a matter involving" Allen to the Pentagon.

Panetta turned the matter over to the Pentagon's inspector general to conduct an investigation into what a defense official said were thousands of pages of documents, many of them emails between Allen and Kelley.

The Associated Press reported that a senior U.S. official said the emails between Allen and Kelley were not sexually explicit or seductive but included pet names such as "sweetheart" or "dear." According to AP, the official said that while much of the communication - including some from Allen to Kelley - is relatively innocuous, some could be construed as unprofessional and would cause a reasonable person to take notice.

That official, as well as others who described the investigation, requested anonymity on grounds that they were not authorized to discuss the situation publicly.

Pentagon officials cautioned against making too much of the number of documents, since some might be from email chains, or brief messages printed out on a whole page.

The FBI decided to turn over the Allen information to the military once the bureau recognized it contained no evidence of a federal crime, said a federal law enforcement official, who spoke to the Associated Press on condition of anonymity.

A senior defense official said that the FBI first notified the Pentagon of the Allen matter at 4:15 p.m. Sunday. The Pentagon's top lawyer, Jeh Johnson, then called Defense Secretary Leon Panetta's chief of staff, Jeremy Bash, about 5 p.m. as Bash and Panetta were flying to Honolulu aboard a military jet to begin a weeklong Asia trip. Bash then informed Panetta.

Allen, who commands 68,000 U.S. troops in Afghanistan, was not suspended from his military position. The White House will soon be deciding how many troops will remain in Afghanistan - and for what purposes - after the U.S.-led combat operation ends in 2014. Allen has provided his recommendations to the White House and is key to those discussions.

Although Allen will remain the commander in Afghanistan, Panetta said that he had asked Obama to delay the general'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 request.

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.

National Security Council spokesman Tommy Vietor said in a statement Tuesday that Obama also believes that the Senate should swiftly confirm Dunford.

The unfolding story caused a commotion on Capitol Hill as well, as lawmakers complained that they should have been told about the Petraeus investigation earlier.

Rep. Peter King, R-N.Y., chairman of the House Homeland Security Committee, called the latest revelations about Allen "a Greek tragedy."

Even though Petraeus has stepped down, Sen. Carl Levin, chairman of the Armed Services Committee, said the retired general should testify about the Sept. 11 attack on the U.S. Consulate in Benghazi, Libya, "if he has relevant information."

Sen. Susan Collins, R-Maine, said it was "absolutely imperative" that Petraeus testify, since he was CIA director during the attack and visited Libya afterward.

Asked by reporters if there was a national security breach with the Petraeus affair, Sen. Dianne Feinstein, chairwoman of the Intelligence Committee, said: "We're going to hold an inquiry. We're going to look at things. I have no evidence that there was at this time."

She said she expected Petraeus to testify - "if not this week, then another week. That's for sure."

Associated Press

WASHINGTON - Acting CIA director Michael Morell is holding meetings on Capitol Hill to explain the CIA's take on events that led David Petraeus to resign last week after acknowledging an affair.

Congressional aides say he met Tuesday with Senate Intelligence Chairwoman Dianne Feinstein and the committee's senior Republican, Sen. Saxby Chambliss, and will meet the heads of the House Intelligence Committee today. FBI deputy director Sean Joyce is also scheduled to brief members today.

Lawmakers are concerned whether Petraeus biographer Paula Broadwell had unauthorized access to classified information.