WASHINGTON — General John Allen, the four-star Marine Corps officer who served until earlier this month as the top commander in Afghanistan, will retire from the military to focus on ‘‘health issues within his family,’’ President Obama said Tuesday.
Allen was caught up in the scandal that led to the resignation of David Petraeus as the director of the Central Intelligence Agency. But in January, the Pentagon officially cleared him of misconduct after an investigation into his exchange of e-mails with Jill Kelley, a Tampa, Fla., woman who was also a friend of Petraeus’s. Allen had gotten to know her when he was the acting head of the Central Command in Tampa.
Obama had nominated Allen to be the supreme commander of NATO, but in the intervening weeks Allen decided to retire.
‘‘I told General Allen that he has my deep, personal appreciation for his extraordinary service over the last 19 months in Afghanistan, as well as his decades of service in the US Marine Corps,’’ Obama said in a statement. ‘‘John Allen is one of America’s finest military leaders, a true patriot, and a man I have come to respect greatly.’’
After Obama’s announcement, Allen released a statement through Pentagon officials saying that ‘‘the reasons for my decision are personal.’’
‘‘I did not come to it lightly or quickly, but given the considerations behind it, I recognized in the end it was the only choice I could make,’’ he said. ‘‘While I won’t go into the details, my primary concern is for the health of my wife, who has sacrificed so much for so long.’’
But there is little doubt that an unexpected obstacle to Allen’s new assignment at NATO was the inquiry by the Pentagon inspector general. Allen had strong support among members of the Senate Armed Services Committee, which would have overseen his confirmation to the NATO job.
But officials noted that, during a confirmation hearing, a senator could have officially requested the e-mails between him and Kelley and that they might have entered the public debate.
Leon Panetta, the departing defense secretary, described Allen in a statement as ‘‘one of the US military’s most outstanding battlefield leaders, a brilliant strategist and an exemplary Marine, and I am deeply grateful for his many years of dedicated service to our country.’’
He added that ‘‘General Allen’s selfless dedication to our troops and to their mission was a source of inspiration to those who served with him, as well as to those of us here at home.’’
Panetta disclosed last week that he had met with Allen and had urged him to take time off with his family before deciding whether to accept the president’s nomination to be the senior NATO commander. The NATO commander oversees both US and allied forces in Europe.
Allen, 59, has ‘‘been under a tremendous amount of pressure, a lot of challenges,’’ Panetta said last week.
The defense secretary cited the demands of command — and the effort to compose recommendations to Obama about future troop levels in Afghanistan — in describing why Allen’s tour had been so challenging.
General Joseph Dunford Jr. succeeded Allen as commander of both the US and international military forces in Afghanistan in a ceremony in Kabul on Feb. 10.