(CNN) -- The spiraling scandal that took down former CIA Director David Petraeus has apparently ensnared another powerful general, as authorities announced that Gen. John Allen is under investigation for allegedly sending inappropriate messages to Jill Kelley, a woman who has been linked to the Petraeus scandal.
Allen, who is the commander of NATO's International Security Assistance Force, has denied any wrongdoing, a senior defense official said.
Details of the latest angle of the scandal that has shaken the highest level of the military were sketchy early Tuesday.
Some details about Allen, the top U.S. commander in Afghanistan, came from an overnight statement by Defense Secretary Leon Panetta, while he was on his way to Australia.
"On Sunday, the Federal Bureau of Investigation referred to the Department of Defense a matter involving General John Allen, Commander of the International Security Assistance Force (or ISAF) in Afghanistan," part of the statement said. "Today, the secretary directed that the matter be referred to the Inspector General of the Department of Defense for investigation."
A defense official told CNN there is a "distinct possibility" that the investigation into Allen is connected to the investigation that led to the resignation of Petraeus.
Allen will still retain his position as the commander of ISAF as the investigation continues, the Pentagon said.
But Panetta asked that Allen's nomination to become NATO's supreme allied commander be put on hold, the statement said.
The confirmation hearing to see if Allen would get that lofty military post was scheduled for Thursday.
Also President Obama has nominated Gen. Joseph Dunford to succeed Allen in his position at ISAF, and Panetta has urged the Senate to move quickly on the nomination.
The investigation into Allen was in its early stages but authorities were looking into some 20,000 to 30,000 pages of documents, the defense official said.
It was not immediately clear Tuesday exactly how Allen may be linked to the Petraeus investigation.
Petraeus, 60, resigned Friday after acknowledging he had an affair with a woman later identified as his biographer, Paula Broadwell, 40, a fellow West Point graduate who spent months studying the general's leadership of U.S. forces in Afghanistan.
The investigation into Petraeus came to light during an FBI investigation of "jealous" e-mails reportedly sent by Broadwell to a woman named Jill Kelley, a government source familiar with the investigation told CNN on Monday.
Now authorities say Allen was under investigation because of communications with Kelley.
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.
Petraeus Probe Could Affect Benghazi Inquiry
Days after Petraeus' resignation stunned Washington, investigators were still gathering information about the four-star Army general who once ran the wars in Iraq and Afghanistan.
FBI agents were at the Charlotte, North Carolina, home of Petraeus' paramour late Monday, said local FBI spokeswoman Shelley Lynch. She declined to say what the agents were doing at Broadwell's home.
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 Petraeus' departure was linked to the congressional inquiry.
Rep. Peter King, R-New York, said elements of the 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 the 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."
The Affair and the e-mails
Broadwell and Petraeus first met in 2006 at Harvard University's Kennedy School of Government, where she was a student, Broadwell wrote in the preface of the biography she co-authored on Petraeus.
She told him about her interest in studying military leadership, and he offered his help.
"I later discovered that he was famous for this type of mentoring and networking, especially with aspiring soldier-scholars," Broadwell wrote.
She traveled to Afghanistan, where she interviewed Petraeus repeatedly.
The actual affair began about two months after Petraeus took over at the CIA in September 2011, according to one Petraeus friend.
It ended about four months ago, and the two last talked about a month ago, the friend said.
The decision to end the relationship was mutual, the friend said
But at some point Broadwell also exchanged e-mails with Kelley.
The FBI joined the investigation when Kelley complained that Broadwell was sending harassing e-mails to her in May, a U.S. official told CNN.
According to a source with knowledge of the e-mails, the messages accused Kelley of untoward behavior with some generals at MacDill Air Force Base in Tampa, Florida where Kelley did volunteer work.
The e-mails detailed the "comings and goings of the generals and Ms. Kelley," said the source, who declined to speak on the record because of sensitivity of the investigation.
Among those believed to be referenced in the e-mails was Petreaus.
But now it seems that there are more, potentially damaging e-mails, that hold information about Allen, a four-star general who took over as the commander of the war effort in Afghanistan last year.
A job he took over from Petreaus.