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Photo: The Canadian Press. All rights reserved.

The home of Paula Broadwell, the woman whose affair with retired Gen. David Petraeus led to his resignation as CIA director, is shown as FBI agents conduct a search inside in the Dilworth neighborhood of Charlotte, N.C., Monday, Nov. 12, 2012. (AP Photo/Chuck Burton)

The sex scandal that led to CIA Director David Petraeus' resignation widened Tuesday, with the top U.S. commander in Afghanistan under investigation for alleged "inappropriate communications" with a woman who received threatening emails from Petraeus' former lover.

Defence Secretary Leon Panetta revealed that the Pentagon had begun an internal investigation into thousands of pages of emails from Gen. John Allen to a second woman involved in the Petraeus case.

Allen succeeded Petraeus as the top American commander in Afghanistan in July 2011, and his nomination to become the next commander of the U.S. European Command and the commander of NATO forces in Europe has been put on hold.

In a White House statement early Tuesday, National Security spokesman Tommy Vietor said President Barack Obama has held Allen's nomination at Panetta's request. Obama, the statement said, "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."

Meanwhile, FBI agents prepared a timeline of the Petraeus affair and searched the home of Paula Broadwell, the 40-year-old biographer with whom the 60-year-old Petraeus had an affair that led to his abrupt resignation Friday.