WASHINGTON (CNN) -- The top U.S. commander in Afghanistan allegedly exchanged "flirtatious" e-mails with a woman who was supposedly being threatened by the CIA director's mistress, according to a Defense Department official.
Now, the commander, Marine Gen. John Allen, is being investigated by the Defense Department, the woman who traded flirty e-mails with Allen is asking for privacy, and the home of the former spy chief's lover has been searched by the FBI.
These are the latest developments in the complicated and widening scandal that began with CIA Director David Petraeus and two women with military connections, and has now ensnared Allen.
It also threatens to bog down a newly re-elected President Barack Obama. His administration is preparing for critical fiscal negotiations with Congress, but instead finds itself facing questions about sex scandals and dealing with powerful lawmakers increasingly concerned about potential security risks and why they weren't told of the Petraeus affair sooner.
"Well, I certainly wouldn't call it welcome," White House spokesman Jay Carney said in facing a blizzard of questions about Petraeus and Allen at Tuesday's press briefing.
The FBI informed defense officials about the allegations involving Allen on Sunday, the Defense Department said, and Defense Secretary Leon Panetta referred the issue to the department's inspector general for investigation.
According to the Defense Department, Allen is under investigation for what one defense official referred to as "flirtatious" e-mail messages with Jill Kelley, the woman whose complaints about anonymous, harassing e-mails led to the discovery of Petraeus' affair with a woman later identified as his biographer, Paula Broadwell.
Military sex scandal heats up
Petraeus, a retired four-star general and Allen's former military boss at the U.S. Central Command, or CENTCOM, resigned Friday from his post at the CIA after acknowledging the affair.
Although Obama continues to have faith in Allen's leadership, he nevertheless put the Marine Corps general's nomination to become NATO's supreme allied commander on hold pending the outcome of the investigation, Carney said.
Allen will retain his post as the commander of U.S. and allied forces in Afghanistan, pending Senate confirmation of a successor, according to the Defense Department. That vote is due Thursday, Senate officials said.
The investigation into Allen is in its early stages, but authorities are looking into some 20,000 to 30,000 pages of documents, a defense official told CNN. It is not clear how many of those include potentially inappropriate communications.
Who is Paula Broadwell?
A U.S. official told CNN on Tuesday that many of the documents could be innocuous, involving routine business that Allen and Kelley were both involved in at the U.S. Central Command.
"In his duties at CENTCOM, Gen. Allen conducted a lot of legitimate business. She (Kelley) did a lot of work with CENTCOM, including Wounded Warriors and such," the official said. "It could be that 29,900 of the documents are legitimate business, and the few remaining raise a few eyebrows."
The potentially inappropriate messages were "flirtatious" in nature, a defense official who has been authorized to speak on the matter told CNN.
Sources familiar with Kelley have said the relationship between the two was not sexual. One said their communications were not of a sexual nature, while another allowed that the e-mails were flirtatious.
That Allen is remaining in command in Afghanistan suggests that there is no criminal issue, another U.S. official told CNN. But the official said the Defense Department's inspector general, an agency watchdog, could still find evidence of criminal conduct.
While the nature of the relationship between Allen and Kelley, if any, is unclear, evidence of an affair could subject the general to military prosecution. Adultery is a violation of military law.
"I think he ought to stay on unless there is some reason put forward that he has done something wrong, and then I think the military leaders will decide then what the actions will be," Sen. Carl Levin, D-Michigan, chairman of the Senate Armed Services Committee, said when asked whether he thought Allen should step down from his Afghanistan job.
Widespread media reports have described Kelley as a liaison at MacDill Air Force Base in Tampa, Florida, where the U.S. Central Command is headquartered. Both Petraeus and Allen were previously stationed at the base. A Central Command spokesman said she is a volunteer with no official position. Kelley has not responded publicly to the latest news.
On Monday, her brother, David Khawam, told CNN affiliate KYW-TV in Philadelphia that she went to authorities because she was scared after receiving the e-mails. He described his sister as a dedicated mother and said it would be "completely uncharacteristic" for her to have an affair.
Both Allen and Petraeus appear to know Kelley's sister, Natalie Khawam. The men wrote letters in support of Khawam in a custody battle, court records show.
One of the sources familiar with Kelley said she first mentioned the alleged harassment in a casual conversation with an FBI agent she knew socially. She did not seek him out specifically for action on the matter, but was happy for the help, the source said. The source added that Kelley did not know at first that the e-mails led to Petraeus.
Earlier, amid national talk about the Petraeus scandal, Kelley, 37, and her husband released a statement saying they have been friends with Petraeus and his family for more than five years and asked for privacy.
The sprawling story continued to sprout new details Tuesday, including a revelation from a senior official close to Allen claiming that it was Allen who received an anonymous e-mail about Kelley, and tipped her off that someone was threatening her.
Other U.S. officials have said Kelley received harassing e-mails that concerned her and went to the FBI.
"There is no affair," the senior official said. "She is a bored rich socialite involved with every single senior commander at CENTCOM, because she worked as an honorary ambassador."
In another bizarre twist, a jogger running in Rock Creek Park in Washington on Sunday found Broadwell's North Carolina license, according to Lt. Bill Kellogg, spokesman for the Maryland-National Capitol Park Police. Police attempted to contact Broadwell, who lives with her husband and children in Charlotte, but were unsuccessful. Because her name has been in the news recently, they also reached out to the FBI.
Meanwhile, the FBI continues to look into the Petraeus affair amid congressional calls for an inquiry into why leaders were not notified of that matter sooner.
The Petraeus scandal also has raised questions about potential impacts on national security, including concerns that his paramour may have had access to his classified schedule and a New York Times report that she had classified documents on her laptop computer.
FBI agents were at Broadwell's Charlotte, North Carolina, home late Monday, said local FBI spokeswoman Shelley Lynch. She declined to say what the agents were doing there.
A source told CNN national security contributor Fran Townsend that Broadwell was acting as Petraeus' archivist, and that the FBI went to the house to look for any documents she might have. It was not clear whether any of the material was classified, the source said.