Gen. Yasar Buyukanit, who heads Turkey's land forces, was accused by a prosecutor in the eastern city of Van, reports Britain's Independent.
The prosecutor claimed the general sought to set up rogue units in the southeast to stoke clashes with Kurdish separatists and security forces, the report said.
Buyukanit is due to become chief of staff in August. The accusations against him were part of an indictment of two soldiers and a Kurdish informer over the bombing of a bookshop on the Iraqi border, killing one man.
Although Turkey's army supports the EU application, the report said some officers feel EU-required reforms would undermine Turkey's secularism, reduce the military's influence and encourage Kurdish separatism and the Islamic movement.