In a new twist to the General David Petraeus sex scandal, the Pentagon said Tuesday that the top American commander in Afghanistan, General John Allen, is under investigation for alleged ‘‘inappropriate communications’’ with a woman who is said to have received threatening e-mails from Paula Broadwell, the woman with whom Petraeus had an extramarital affair.
Defense Secretary Leon Panetta said in a written statement issued to reporters aboard his aircraft, en route from Honolulu to Perth, Australia, that the FBI referred the matter to the Pentagon on Sunday.
Panetta said that he ordered a Pentagon investigation of Allen on Monday.
A senior defense official traveling with Panetta said Allen’s communications were with Jill Kelley, who has been described as an unpaid social liaison at MacDill Air Force Base, Fla., which is headquarters to the US Central Command. She is not a US government employee.
Kelley is said to have received threatening e-mails from Broadwell, who is Petraeus’s biographer and who had an extramarital affair with Petraeus that reportedly began after he became CIA director in September 2011.
Petraeus resigned as CIA director on Friday.
Allen, a four-star Marine general, succeeded Petraeus as the top American commander in Afghanistan in July 2011.
The senior official, who discussed the matter only on condition of anonymity because it is under investigation, said Panetta believed it was prudent to launch a Pentagon investigation, although the official would not explain the nature of Allen’s problematic communications.
The official said 20,000 to 30,000 pages of e-mails and other documents from Allen’s communications with Kelley between 2010 and 2012 are under review. He would not say whether they involved sexual matters or whether they are thought to include unauthorized disclosures of classified information. He said he did not know whether Petraeus is mentioned in the e-mails.
In Charlotte, N.C., Monday night, FBI agents searched Broadwell’s North Carolina home. FBI spokeswoman Shelley Lynch declined to say what the agents were doing there.
Earlier Monday, an aide to Eric Cantor, the House majority leader, said that the Virginia representative first heard about Petraeus’s extramarital affair on Oct. 27 from an FBI source he didn’t know.
Communications director Rory Cooper said Cantor notified the FBI’s chief of staff of the conversation, but did not tell anyone else because he did not know whether the information from an unknown source was credible.
On Oct. 31, Cantor’s chief of staff called the FBI chief of staff to relay information and received a return call from the official the next day. The Cantor aide was told the FBI could not confirm or deny an investigation, but the bureau official assured the leader’s office it was acting to protect national security.
Cooper said Cantor’s office did not notify anyone else because, ‘‘at the time, it was one person making the allegation which, while serious, was completely unsubstantiated. He [Cantor] didn’t know this person. He did the only thing he thought appropriate and that he thought was responsible. Two weeks ago, you don’t want to start spreading something you can’t confirm.’’
Cantor believed that if the information was accurate and national security was affected, the FBI would — as obligated — inform the congressional intelligence committees and others, including House Speaker John Boehner.