Local government authorities have suspended activities for a total of 714 churches in different parts of Kigali over the last one week for failure to meet minimum standards.
The places of worship were found to lack basic infrastructure, fell short of hygiene, safety standards and had issues related to their legal status, according to local leaders.
The crackdown is being carried out by respective urban district authorities in partnership with the Rwanda Governance Board.
According to Justus Kangwagye, the Head of Political Parties and Civil Society Department at the Rwanda Governance Board, places of worship are required to meet basic requirements in terms of safety, hygiene, infrastructure and legality which those affected were found to be lacking.
In an interview on Monday, Kangwagye said most of the affected places of worship were asked to halt operations until they meet the expected standards.
"Worshiping should be done in an organised way and meet minimum standards. Exercising your freedom of worship should not encroach on other people's rights. They have been asked to halt operations until they meet the requirements," he said.
Some may not be able to resume operations any time soon, he said.
Kangwagye said some premises exposed worshipers to risks.
"For instance, if the infrastructure is deemed likely to cause danger to those worshiping, it is obvious that it fails to meet the requirements," he explained.
Others were found to have inadequacies such as lack of parking lots which would lead to their members parking by the roadsides and causing traffic jam.
Other churches which were closed operated from tents.
"Churches that are hosted in tents were also asked to review their premises before they can continue their operations. As for hygiene and sanitation, you cannot have a gathering where there is no water for washing hands, no toilets among other issues," he said.
Others, he added, were warned on the lack of safety and security installations and asked to look into it or risk closure.
For instance, a number of churches were found not to have metal detectors for security measures, which is a requirement, or a lightening arrestor.
Heads of such churches were also put on notice to make the necessary adjustments.
The authorities also issued a warning to churches that make noise and disturb peace in residential neighbourhoods.
On legality, Kangwagye explained that setting up a church, requires a temporary certificate which expires after 12 months.
However, one is required to make an application for formalising their operations within nine months of opening before the expiry of the temporary certificate.
"Most failed to honour this and failed to apply for permanent [operation] documents. They cannot be allowed to operate outside the law," the RGB official said.
Some churches, according to him, were hiding behind freedom of worship in breach of the law.
The directive has not only affected Christian places of worship as a mosque was also affected.
Emmanuel Bayingana, the vice mayor in charge of social affairs in Kicukiro District where 156 out of 352 churches were closed down, told The New Times that hygiene and infrastructure levels of those that were closed were found lacking.
Bayingana said that some of the churches will not be able to resume operations as they have inadequate structures and operate from tents.
"Some of them are unlikely to resume operations as they have been operating way below required minimum requirements," he said.
Langwide Nyirabahire, the vice mayor in charge of Social affairs in Gasabo District, said that over 355 churches have been closed so far but the process of assessment was still ongoing.
Gasabo has 699 churches.
In Nyarugenge, out of 300 churches, 203 of them have since been closed down for failure to meet standards.
City residents expressed mixed reactions with some saying the move is waranted to protect the general public while others said churches ought to have been given more time to comply with the directives or seek appropriate locations.
Bishop Innocent Nzeyimana, the president of the Churches' Forum in Nyarugenge District, pleaded on behalf of the churches that those lacking slight requirements should be reopened and allowed to operate as they fix issues raised.