The court said there was no evidence that the justice minister of former Bosnian Serb leader Radovan Karadzic was responsible for war crimes against Bosnian Muslims at several detention camps.
Mandic was also cleared of charges of planning and leading an attack by Bosnian Serb police and paramilitary units on a Sarajevo police training centre.
Last year Mandic was jailed for five years for abuse of office and fraud at a bank he used to manage.
Mandic left Bosnia towards the end of the war and moved to Belgrade where he became a wealthy businessman. He was arrested
in Montenegro in 2005 and transferred to Bosnia.