About 10 hotels, pubs and club houses were also closed, officials said.
Some estimates put Lagos' population at around 20 million, creating a constant background of noise - from the blaring of car horns, to the Muslim call to prayer and loud singing in churches.
The state government has vowed to make the city, the biggest in Africa, noise-free by 2020.
In August, the Lagos State Environmental Protection Agency (LEPA) closed 22 premises after residents complained about noise emanating from them.
Following the latest crackdown, its general manager Bola Shabi said the agency would no longer allow people to pray in makeshift buildings and tents.
Mr Shabi said noise levels had been reduced by about 35%, but this was not a "pass mark yet".
"Enforcement is a continuous exercise and we have set a target for ourselves. We want to ensure that Lagos is noise-free by the year 2020," he said.
Mr Shabi said mosques complied with their instructions more than churches because when they are ordered to shut down, they "instantly bring down their speakers or reduce the noise they make''.
Nigerians are extremely religious, with a large number of evangelical churches operating in Lagos.
Christians form the majority in the city.
In 2014, 116 people died when a building owned by popular televangelist TB Joshua collapsed in Lagos.