Two others—Brigadier-General Gen Wilson Gumisiriza and Major Wilson Ukwishaka—pleaded not guilty.
The officers are jointly accused of murder and complicity to murder as a war crime.
Prosecution asked the court to order temporary detention of the officers because investigations were still underway. A ruling was expected today.
According to prosecution, Gumisiriza was the officer in charge of the operation of evacuating the priests, who were taken to another place in Ruhango district, where they were killed on June 4, 1994.
Ukwishaka was the platoon commander of that force.
The last week’s arrests follow disclosure by the Prosecutor of International Criminal Tribunal for Rwanda (ICTR), Justice Hassan Jallow, before the UN Security Council on 4 June that some soldiers of RPF had committed atrocities during the genocide when tabling his six-monthly report on the court’s exit strategy. The UN has estimated that about 800,000 ethnic Tutsis and moderate Hutus were killed in the April-July slaughter.
RPF, now Rwanda Defence Force (RDF) is currently in power under President Paul Kagame.
Rwanda shared concurrent jurisdiction with the tribunal over such offences and the ICTR will monitor the trial, according to Justice Jallow.
Justice Jallow’s predecessor, Swiss Carla Del Ponte, was the first to disclose over the RPF investigations during her tenure as the ICTR prosecutor between 1999 and 2003.
The Rwandan government in the past has been furious over the investigations and even reached a boiling point by refusing to co-operate with the UN tribunal and once even denied entry visa to Carla Del Ponte.