Rwanda has banned mosques in the capital, Kigali, from using loudspeakers during the call to prayer.
They say the calls, made five times a day, have been disturbing residents of the Nyarugenge district, home to the capital's biggest mosques.
But an official from a Muslim association criticised it, saying they could instead keep the volume down.
Some 1,500 churches have been closed for not complying with building regulations and noise pollution.
The majority of Rwandans are Christian. Muslims make up around 5% of the population.
The government says the Muslim community has complied with the ban.
Analysis: Rwanda's open secret
Ally Yusuf Mugenzi: Editor of BBC Great Lakes service
To understand the latest round of regulations imposed by Rwandan authorities on religious groups, we have to look back to the 1994 genocide, in which some 800,000 people were killed.
A number of the Roman Catholic churches, where thousands of Tutsis had taken refuge, became killing grounds during the 100-day rampage.
Rwandans lost faith in the powerful institution and gravitated towards Pentecostalism and Islam.
Today's noise pollution concerns have silenced the loudspeakers on Kigali's mosques. But it would be wrong to say that Muslims are being targeted. They can still go to mosques and pray five times a day.
The same cannot be said for the Pentecostals.
About 1,500 Pentecostal churches across the country have been closed over the past month, leaving worshippers with nowhere to pray.
This might have something to do with Rwanda's open secret: the country's religious denominations are expected to pledge loyalty to the government of long-time President Paul Kagame.
Pentecostal leaders might not be toeing the line.
But the authorities are right to focus on those churches' disregard for building regulations. Many of them hold noisy services, are badly constructed, situated in residential homes, and are a legitimate health and safety concern.
"I have found that they have begun to respect it and it has not stopped their followers from going to pray according to their praying time," Havuguziga Charles, a local official from Nyarugenge told the BBC's Great Lakes service.
This comes as the government continues its clampdown on substandard churches across the East African country.
Most of them were small Pentecostal churches, and one mosque was also closed.
The government says the reason is that some preachers "deceive their congregation with misleading sermons", AFP reports.
But some preachers have accused the government of trying to control their message to congregants in a country accused by human rights groups of stifling free speech.