Allen, 58 and married, was nominated in October by President Barack Obama to be Supreme Allied Commander Europe and commander of the U.S. European Command. That nomination is now on hold, but Allen will remain commander of U.S. forces and the NATO International Security Assistance Force in Afghanistan, the official said.

( PHOTOS: Who’s who in the Petraeus scandal)

The FBI notified the Defense Department on Sunday of “potentially inappropriate communications” between Allen and Kelley, and turned over to Pentagon lawyers 20,000 to 30,000 pages of emails exchanged by the two from 2010 to 2012.

The email web has now ensnared two of the biggest stars of the U.S. national-security establishment, and two of the commanders in America’s longest war. Allen succeeded Petraeus as commander in Afghanistan in July 2011. Before that, Allen had been based in Tampa as deputy commander of the U.S. Central Command.

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From late 2008 until mid-2010, Allen was deputy commander at CENTCOM while Petraeus was commander.

Kelley, 37, who had complained of threatening emails from Petraeus biographer Paula Broadwell, has been described as a Tampa socialite and friend of Petraeus who was viewed by Broadwell as a potential romantic rival.

( PHOTOS: General David Petraeus’s career)

Kelley’s complaint to an FBI agent about the emails touched off the investigation that led to the resignation of Petraeus, 60, on Friday.

Allen holds one of the highest profile and most sensitive positions in the military, consulting with President Barack Obama, Defense Secretary Leon Panetta and Afghan President Hamid Karzai as the U.S. prepares to transition control of the country’s security to Afghans. The U.S. has about 68,000 troops in Afghanistan, and the total NATO force numbers about 100,000.

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Panetta, now on an Asia-Pacific swing, was flying from Hawaii on Sunday when the FBI contacted his general counsel, who was aboard the plane, about the emails at about 5 p.m. ET Sunday. The secretary’s senior advisers immediately told him of the call, and the White House was also notified, the official said.

“Preliminary review of the documents raised enough concerns about inappropriate communications that the prudent step was to initiate an investigation,” the official said. “General Allen has disputed any wrongdoing in this matter. The department’s very strong intention is that he receive a fair hearing. He will remain commander of ISAF while we look at this matter further.”

Panetta asked that the chairman of the Joint Chiefs of Staff, Army Gen. Martin Dempsey, be notified, and Pentagon lawyers began reviewing the emails provided by the FBI. Around noon Monday, the matter was referred to the department’s inspector general, and a delay was sought in the nomination.

( Also on POLITICO: Ret. Gen.: Allen’s ‘bizarre’ behavior)

Allen’s confirmation hearing for Supreme Allied Commander had been set for Thursday before the Senate Armed Services Committee. Allen, who graduated from the Naval Academy in 1976, is based in Kabul, the capital of Afghanistan, but is currently in Washington, where he was preparing for the hearing, the official said.

The department disclosed the investigation to the press as Panetta flew from Honolulu to Perth, Australia, for a defense summit.

( Also on POLITICO: Petraeus affair timeline of events)

Officials expect that Allen will return to lead the fight, the official told POLITICO.

“Just because there are allegations out there doesn’t mean you pull a commander,” the official said. “The picture hasn’t been filled in. We believe that it’s prudent for the war effort to maintain his leadership while this matter is being reviewed. If we learn new information that causes us to adjust course, we will.”

( Also on POLITICO: Petraeus, Broadwell’s email secret)

On Monday evening, the Pentagon disclosed the investigation to Senate Armed Service Chairman Carl Levin (D-Mich.) and other members of the committee, and the House Armed Services Committee, with the Senate calls complete by 10:15 p.m. and the House calls complete by 11 p.m.

When Allen was nominated in October, Obama said in a written statement: “I have personally relied on his counsel and am grateful for his devotion to our national security and to the safety of the men and women with whom he serves. Under General Allen’s command, we have made important progress towards our core goal of defeating Al Qaeda and ensuring they can never return to a sovereign Afghanistan.“

( See also: Complete coverage of David Petraeus)

At the same time, Gen. Joseph Dunford was nominated to succeed Allen as ISAF commander. Dunford is currently the assistant commandant of the Marine Corps. His confirmation hearing was set for the same time as Allen’s — Thursday at 9:30 a.m. Allen, who has been commander in Afghanistan since July 2011, was to replace Adm. Jim Stavridis in the spring.