The Catholic parish of Ruhengeri in the north of the country, where the priests are stationed, also risks closure.
The two priests, Father Emmanuel Ndagijimana and Father Felicien Nsengiyumva, are said to have failed to adhere to the number of congregants allowed to attend mass.
Police found “a chaotic situation” in the church and “everyone there was at high risk of infection”, according to a government statement.
“We remind religious denominations particularly those that were permitted to resume services to follow strict safety guidelines as issued by relevant authorities,” the statement said.
Rwanda’s cabinet approved the reopening of worship places in July but under strict safety measures. Worshippers have to wear face masks, get their temperatures measured and maintain social distance.