By Michael Pearson
(CNN) — 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 e-mails from another woman led to the discovery of Petraeus’ affair 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.
The defense official said there is a “distinct possibility” that the investigation into Allen is connected to the one that led to Petraeus’ resignation.
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. 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.
Petraeus probe could affect Benghazi inquiry
Days after his resignation stunned Washington, investigators were still gathering information about Petraeus, who once ran the wars in Iraq and Afghanistan.
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.
Also, a video has surfaced of a speech by Broadwell in which she suggested the Libya attack on September 11 was targeting a secret prison at the Benghazi consulate annex, raising unverified concerns about possible security leaks.
“I don’t know if a lot of you have heard this, but the CIA annex had actually taken a couple of Libyan militia members prisoner and they think that the attack on the consulate was an effort to get these prisoners back,” said Broadwell in a speech last month at the University of Denver.
A senior intelligence official told CNN on Monday, “These detention claims are categorically not true. Nobody was ever held at the annex before, during, or after the attacks.”
Broadwell’s source for that previously unpublished bit of information remains unclear, and there’s no evidence so far that it came from Petraeus.
Administration officials have said the Benghazi assault was a terrorist attack.
Along with questions about Broadwell’s access, the Petraeus scandal also presents challenges to the congressional inquiry into the Benghazi attack.
Petraeus recently traveled to Libya to meet the CIA station chief to discuss the attack, CNN has confirmed. He was scheduled to testify before a congressional committee this week on the assault and the U.S. government response to it.
That now will not happen, but it is possible that he could be summoned by Congress to testify later.
Some Republicans have criticized the administration’s response to the Benghazi attack and have speculated that the timing of Petraeus’ departure was linked to the congressional inquiry.
Rep. Peter King, R-New York, said elements of the general’s story “don’t add up.” He called Petraeus “an absolutely essential witness, maybe more than anybody else.”
However, a senior U.S. official said Petraeus’ departure wasn’t connected to the Benghazi hearing.
“Director Petraeus’ frank and forthright letter of resignation stands on its own,” said the official, who spoke on condition of anonymity because of the sensitivity of the topic. “Any suggestion that his departure has anything to do with criticism about Benghazi is completely baseless.”
On Tuesday, Panetta, who preceded Petraeus at the CIA, called his successor’s downfall “a very sad situation.”
He also agreed with congressional calls for an inquiry into the FBI investigation that led to Petraeus’ resignation. Some congressional leaders have said the agency failed to notify key leaders quickly enough.
“That’s another issue I think we ought to look at, because as a former director of the CIA and having worked very closely with the intelligence committees, I believe that there is a responsibility to make sure that the intelligence committees are informed of issues that could affect… the security of those intelligence operations,” he told reporters while traveling in Australia.
Sen. Dianne Feinstein, D-California, said on “Fox News Sunday” that she would push the FBI for answers, saying she and other congressional leaders should have been told because Petraeus’ involvement “could have had an effect on national security.”
She told NBC that leading members of the House and Senate intelligence committees are usually briefed on “operationally sensitive matters,” but were not in this case.
Section 501 of the National Security Act of 1947 spells out the requirements for the executive branch to inform the congressional intelligence committees of key intelligence-related activities.
“The president shall ensure that the congressional intelligence committees are kept fully and currently informed on the intelligence activities of the United States, including any significant anticipated intelligence activity as required by this title,” the statute reads.
Rep. Tom Price, R-Georgia, said Tuesday on CNN’s “Starting Point” that the Obama administration has many questions to answer.
“This administration and these individuals need to answer questions about whether there was any compromise in American intelligence or security,” he said.
Rep. Debbie Wasserman Schultz of Florida, who chairs the Democratic National Committee, also told “Starting Point” that congressional leaders should have been told sooner and that an investigation is warranted. But she warned against turning it into another partisan firefight.
“Let’s not have this spiral downward into something that just becomes more politics. We just came off an election,” she said.
™ & © 2012 Cable News Network, Inc., a Time Warner Company. All rights reserved.