Twenty four soldiers and former servicemen are accused of murder of about 30 persons allegedly belonging to the opposition.They were arrested in September 2006.
However, only 14 accused were present before the tribunal.
The President of Tribunal, Colonel Leonidas Nkurunziza, said the decision took into consideration the constitution, penal code and code reorganizing the jurisdiction of military tribunals.
It is alleged that the victims were murdered and later hurled into nearby Ruvubu River.
The key architect of the alleged killings, Colonel Vital Bangirimana, who was then commander, has already fled the country since November and was sought under an international arrest warrant.
According to the President of Association for Promotion of human and Prisoner Rights (APRODH), Pierre Claver Mbonimpa, only the International Criminal Court (ICC) was an appropriate body to try the case.
Mbonimpa said that he was disappointed the way in which the case proceeded. "The national courts are unable to try the case, it is necessary to transfer it to ICC...we request its intervention", he said.
© Hirondelle News Agency