He was arrested last month in Bujumbura, on the eve of his 51st birthday.
Witnesses have told AFP that Bunyoni appeared in court clad in green prison uniforms and handcuffed. The court extended his pre-trial detention at Ngozi Prison in the north of the country.
Bunyoni, a former police chief and minister of internal security, was replaced by Gervais Ndirakobuca after President Evariste Ndayishimiye took office.
Ndayishimiye had warned of a "coup" plot against him, and Bunyoni was seen as the head of a group of military leaders known as "the generals" who wielded political power in Burundi.
Bunyoni’s charges include undermining the internal security of the state, undermining the proper functioning of the national economy, illegal enrichment, illegal possession of weapons, and insulting the president.