The scandal that took down former CIA Director David Petraeus has ensnared another powerful general.
Gen. John Allen, the top U.S. commander in Afghanistan, is under investigation by the Defense Department for allegedly sending inappropriate messages to Jill Kelley, the woman whose complaints about receiving anonymous, harassing e-mails led to the discovery of Petraeus' affair with Paula Broadwell and his eventual resignation.
While details remained sketchy Tuesday, President Barack Obama ordered that Allen's nomination to become NATO's supreme allied commander be put on hold pending the outcome of the investigation. He 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.
Allen has denied any wrongdoing, a senior defense official said.
The newest revelation adds another wrinkle to an unfolding drama that has shaken the military and Congress, where some have called for an inquiry into why congressional officials were not told sooner of the FBI investigation that uncovered Petraeus' extramarital affair.
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.
More details could surface Tuesday during news briefings at the White House and the Pentagon, scheduled for the afternoon.
Petraeus, a retired four-star general, resigned Friday from his post at the CIA after acknowledging an affair with a woman later identified as his biographer, Paula Broadwell. His resignation came just days before he was to testify to Congress on the September 11 attack on the U.S. Consulate in Benghazi, Libya, that killed four Americans.
The FBI launched the investigation after Kelley contacted the agency about anonymous, harassing e-mails she had received, a U.S. official told CNN. Investigators eventually traced them to Broadwell, the official said. A different U.S. official described the e-mails as "jealous."
The FBI informed defense officials about the allegations involving Allen on Sunday, the Defense Department said in a statement. Defense Secretary Leon Panetta referred the issue to the department's Inspector General for investigation, according to the statement.
The investigation into Allen is in its early stages, but authorities are looking into 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.
A U.S. official told CNN Tuesday that many of the documents could be innocuous, involving routine business that Allen and Kelley were both involved in at Central Command, or CENTCOM.
"In his duties at CENTCOM, Gen. Allen conducted a lot of legitimate business. She 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.
"There was no security information exchanged, there was nothing hateful in the messages," that official said. "It was not threatening."
It was not immediately clear how the two investigations might be linked, but widespread media reports indicate Kelley is an unpaid 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.
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.
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 could still find evidence of criminal conduct.
Kelley has not responded publicly to the latest news.
On Monday, her brother, David Khawam, told CNN affiliate KYW-TV 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.
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.
Obama accepted Panetta's recommendation to delay Allen's nomination to lead NATO, National Security Council spokesman Tommy Vietor said Tuesday.
"The president remains focused on fully supporting our extraordinary troops and coalition partners in Afghanistan, who Gen. Allen continues to lead as he has so ably done for over a year," Vietor said.
Obama has nominated Gen. Joseph Dunford to succeed Allen to command U.S. and allied forces in Afghanistan, and Vietor said the president wants the Senate to act quickly to confirm the appointment.