Gatsibo District leaders closed 75 churches, and two mosques whose standards were found lacking following a two-week inspection.
The district assessed 646 churches, and only 210 were found to meet required standards, officials said.
At a meeting with clerics on Wednesday, district leaders said some 393 other churches were given 15 days to fix the issues raised, such as painting, pavements, among others to avoid being closed.
Up to 40 mosques were assessed.
Gatsibo mayor Richard Gasana explained that the assessment looked at hygiene and infrastructure, among other things.
"We met with more than 180 representatives of the churches, we showed them how some churches are on verge of collapse, some operated in makeshift tents, which posed a threat to worshipers," he said.
The mayor told residents that government intervention in faith affairs was in their interest.
"This is because if something terrible happens, such as church collapse, we are the ones to be asked," he said.