Mahmoud Velitov, the imam of Moscow's Yardyam Mosque, has been arrested on charges of inciting terrorism, an unidentified source in law enforcement told the Interfax news agency on Tuesday.
Velitov was arrested on Tuesday by the special services and is being interrogated by the Russian Investigative Committee, according to the source.
The charge carries a prison sentence of between two and five years.
The Yardyam Mosque was built between 1996 and 1997 and is situated in the north of Moscow. It has a capacity of around 2,000 people and is one of only four mosques in the city.
Moscow Mayor Sergei Sobyanin said during his election campaign in 2013 that no more mosques would be built in Moscow. He said that the city cannot provide them for communities that will remain in the area temporarily.
Separately, a package of amendments to Russian anti-terrorist legislation, put forward by ultraconservative United Russia lawmaker Irina Yarovaya, were signed by President Vladimir Putin last week.
The package introduces a number of new laws, including restrictions on religious activity, increases the number of crimes with which children aged between 14 and 17 can be charged, and the ability to prosecute citizens for not informing law enforcement of terrorist activities.