In January, Allen was cleared by Pentagon investigators of allegations of professional misconduct over email exchanges with a Florida socialite. Allen had commanded US and NATO forces in Afghanistan.

"Today, I met with General John Allen and accepted his request to retire from the military so that he can address health issues within his family," Obama said in a statement.

The decision by the Defense Department's Inspector General helped lift a cloud that had hung over Allen, who is married and has two daughters, since he became ensnared in the scandal that forced retired General David Petraeus to resign as CIA director in November.

The Pentagon inquiry centered on emails between Allen and Jill Kelley, a Tampa, Florida, resident who knew Allen when he served as the No. 2 officer at the US military's Tampa-based Central Command from July 2008 to June 2011.

The Kelley-Allen emails surfaced when the FBI investigated Kelley's allegations of receiving anonymous, harassing emails from someone else about Petraeus. Those other emails led the FBI to uncover an extramarital affair between Petraeus and his biographer, Paula Broadwell.