During the 1990s war in Bosnia-Herzegovina, the 50-year-old Jankovic was deputy military police commander and one of the top paramilitary leaders in Foca, a town southeast of Sarajevo.
He was charged on personal and command responsibility with seven counts of crimes against humanity and seven counts of violations of the laws and customs of war, including the abuse and rape of Muslim women.
Jankovic surrendered to the UN court last March and in April entered a plea of not guilty.
Chief prosecutor Carla del Ponte asked that the case against him be transferred to the Bosnian judiciary in line with the Hague tribunal's exit strategy, under which all trials must end by 2008.
The tribunal approved del Ponte's request today.