WASHINGTON — An FBI investigation that led to the resignation of Gen David Petraeus also turned up evidence that Gen John Allen, the top U.S. commander in Afghanistan, was exchanging potentially inappropriate emails with a Florida woman involved in the scandal, Pentagon officials said.

Defense Secretary Leon Panetta said in a statement early Tuesday that he had ordered an investigation of Allen after the FBI informed the Pentagon it had uncovered thousands of pages of emails between Allen and Jill Kelley, a 37-year old who has been described as an unpaid social liaison at MacDill Air Force Base, Fla., which is headquarters to the U.S. Central Command.

Kelley's complaints to the FBI that she had received anonymous e-mails warning her to stay away from Petraeus led the FBI to open an investigation that ultimately traced the e-mails to Paula Broadwell, Petraeus’s biographer, who was involved in an affair with Petraeus.

The latest twist in the scandal investigation, coming only days after Petraeus resigned as CIA director after admitting he had a extramarital affair, has thrown President Obama’s national security team into turmoil and focused attention on the private lives of the nation’s most senior military commanders.

One official said that Allen who is married, had denied having an inappropriate relationship with Kelley, who is married to a Tampa doctor and known among officers at Central Command for hosting social events and for forging social ties with top commanders in Tampa. Allen was deputy head of Central Command before taking command in Afghanistan last year.

Officials refused to describe the nature of the emails between Kelley and Allen, who replaced Petraeus as the top commander in Afghanistan and was nominated in October by President Obama to take over as Supreme Allied Commander in Europe. Panetta asked the Senate to place Allen nomination on hold until after the investigation is complete.

A spokesman for Allen, who has been in Washington preparing for his confirmation hearings, had no comment on the investigation. Efforts to reach Kelley were also unsuccessful. She was last year given an award for her support to Central Command and was named an honorary ambassador for the command, an unpaid position with no official duties.

But Kelley has angered some senior officers by her persistent efforts to forge close personal ties to successive Central Command four-star officers, by deluging with emails. After being named honorary ambassador, she asked the command for staff at the headquarters to help her organize social functions, a former U.S. official said.

Panetta said that Allen would remain in command in Afghanistan while the investigation into the email by the Defense Department inspector general is conducted.

The FBI's decision to refer the matter to the Pentagon, along with Panetta's decision to allow Allen to continue as commander of U.S. and international forces in Afghanistan, suggested that officials viewed the matter as a possible infraction of military rules rather than a violation of federal criminal law.

“His leadership has been instrumental in achieving the significant progress that ISAF, working alongside our Afghan partners, has made in bringing greater security to the Afghan people, Panetta said. “He is entitled to due process in this matter.”

At the same time, Panetta urged the Senate to move ahead on confirmation hearings for Gen. Joseph Dunford, the Marine who has been selected by Obama to succeed Allen in Kabul.

The last three U.S commander in Afghanistan - Petraeus, Allen, and Gen. Stanley McChrystal - have all now come under scrutiny for their personal behavior, although Petraeus’s affairs apparently began after he stepped down in Afghanistan. McChrystal was fired by Obama after a magazine article that appeared to show him and his staff criticizing and making crude jokes about Obama’s top civilian advisors.