Rights office spokesman Rupert Colville said Tuesday that Anders Kompass resigned "several weeks ago" though the resignation won't take effect before August.
The UN internal justice system in January cleared Kompass, a Swede who was the operations director of the rights office, over the leaks in 2014 about accusations that French soldiers had abused some children they were sent to protect in CAR.
Their deployment was independent of the United Nations. French authorities say they are investigating the allegations and have vowed to punish anyone found responsible.
