Lt. Col. Les Carroll, a spokesman for the International Security Assistance Force in Afghanistan, said Allen returned to work on Wednesday.
Allen had been in Washington when news of his problematic email correspondence with Florida socialite Jill Kelley surfaced last Monday. He was expected to testify before a Senate committee last Thursday on his nomination to become the commander of U.S. European Command and the top NATO general. Defense Secretary Leon Panetta has put that nomination on hold.
At the time Panetta announced that the Pentagon inspector general is reviewing as many as 30,000 pages of Allen's correspondence with Kelley, Panetta said he had determined that Allen should remain in command in Kabul, pending the outcome of the probe.
Allen's predecessor as Afghanistan war commander, David Petraeus, resigned from his post as CIA director earlier this month after acknowledging an extramarital affair with his biographer, Paula Broadwell. The FBI learned of the affair as it investigated anonymous, harassing emails, ultimately traced to Broadwell, that were sent to Kelley.
The FBI investigation also turned up the emails between Allen and Kelley.