A statement availed to independent Hirondelle Agency by the army's spokesman, Major Jill Rutaremara, said that "the suspects will appear in court soon."
The arrested are Brigadier-General Wilson Gumisiriza, Major Wilson Ukwishaka, Captain John Butera and Captain (retired) Dieudonne Rukeba.
Among the 13 killed clergymen included Archbishop of Kigali Vincent Nsengiyumva, Bishop of Byumba Joseph Ruzindana and Bishop of Kabgayi, Thadee Nsengiyumya, who was also then President of the Conference of Catholic Bishops of Rwanda.
The arrests follow last week's disclosure by the Prosecutor of International Criminal Tribunal for Rwanda (ICTR), Justice Hassan Jallow, before the UN Security Council that some soldiers of the Rwanda Patriotic Front (RPF) had committed atrocities during the genocide. The UN has estimated that about 800,000 ethnic Tutsis and moderate Hutus were killed in the April-July slaughter.
"It has been established that on 5 June, 1994, RPF soldiers had killed 13 clergymen and two other civilians at Gitarama [central Rwanda]", Mr Jallow told the UN when tabling his six-monthly report of the Court's exit strategy.
RPF is currently in power under President Paul Kagame.
Justice Jallow added that some of the perpetrators are reportedly to have died, while others are serving within the Rwanda army.
Rwanda shared concurrent jurisdiction with the tribunal over such offences and the ICTR will monitor the trial, he said.
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.
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© Hirondelle News Agency