The men attacked an examination centre housing 35 final year students in Isiro town, the capital of Haut-Uélé province.
The students went on to sit for the examinations on Monday, according to a priest in the area.
Hundreds of students fled after an attack near another examination centre, according to AFP news agency.
Some 700 students and teachers fled after the attack near the border with South Sudan.
The militia wanted to sabotage exams, the agency quotes a local army spokesperson Dieudonne Kasereka as saying.
BBC