“Whatever the affair’s effect had on national security is worth knowing about,” said Sen. Lindsey Graham, R-S.C. “Why did the FBI investigate to begin with? And did this have an effect on national security?”

Allen’s connection to the scandal became known on Tuesday after Defense Secretary Leon Panetta announced while flying to Asia that he’d asked the Pentagon inspector general’s office to investigate the emails between the four-star Marine general and Kelley.

Kelley had been an honorary ambassador to the U.S. Central Command in Tampa, where Allen served as second in command before his June 2011 promotion to oversee the war in Afghanistan. Army Lt. Col. T.J. Taylor, a CENTCOM spokesman, said that Kelley had no official position at the command.

“She is a volunteer and a private citizen, not an employee,” he said. “Because of this, and because there is an ongoing investigation, we have no additional information to provide.”

The contents of those emails were not revealed, although a Pentagon official briefed on them said they contained possibly flirtatious language, such terms as “sweetheart,” which he noted could also have been a sign of a casual manner of address.

The official requested anonymity because he was not authorized to discuss the matter publicly.

A second Pentagon official, who requested anonymity for the same reason, told reporters that the emails weren’t “security related. They’re not, I don’t know, information about acquisition or contracting. They’re not hate or threatening.”

The FBI investigation that uncovered Petraeus’ affair with Broadwell began when Kelley sought help from an FBI agent after receiving what she described as anonymous and threatening emails warning her to stay away from Petraeus.

The probe led to Broadwell as the sender. She is an Army reservist, a West Point graduate and researcher who met Petraeus when he made an appearance at Harvard University.

For his part, Allen has maintained that he had done nothing inappropriate, the Pentagon officials said.

The extent of the friendships maintained with Kelley by Allen and Petraeus was highlighted by the generals’ intervention in a child custody battle involving Kelley’s twin sister, Natalie Khawam.

In their letters, which were first reported by the New York Post, Allen and Petraeus urged the judge overseeing the case to grant Khawam, who lost custody of her child to her ex-husband, more opportunities to spend time with her child.

“We have on many occasions observed Natalie and her son … including when we hosted them and the Kelley family for Christmas dinner this past year. In each case, we have seen a very loving relationship,” Petraeus wrote in a Sept. 20, 2012, letter. “Natalie clearly dotes on her son and goes to great lengths — and great expense — to spend quality time with him.”

Petraeus and his wife, Holly, became friends with Kelley and her husband while serving as CENTCOM commander from October 2008 and June 2010; he had known Khawam for three years.

He had served as CIA director for more than a year when he sent the letter. But he chose to write it on Army stationery embossed with a four-star flag, symbolizing his four-star rank at the time he retired from the military in July 2011. He also signed the letter as “General, U.S. Army (retired).”

In his letter, Allen said that he and his wife, Kathy, became friends with Khawam while he served as deputy CENTCOM commander from July 2008 to June 2011. He and his wife, he wrote, had seen Natalie and her son on “multiple occasions” during official CENTCOM functions.

In the halls and corridors of the Pentagon, there was little on-the-record talk of the scandal, although in private moments the situation was described time and again as “sad,” “unfortunate” and even “pathetic.”

Around the capital, there was speculation that, regardless of the results of the Allen investigation, he might not rebound quickly from this latest turn in the scandal.

Carney said the White House learned about the Allen emails on Friday after the Justice Department notified the White House counsel that there “may be an issue” in relation to his nomination.

Obama had not spoken directly to Allen, Carney said, and he was uncertain whether Allen had talked with Panetta.

Information from The Associated Press was used in this report.