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.