Mayor Sergei Sobyanin spoke out against construction of a large number of mosques for the city's booming Muslim population because many worshippers are not Muscovites.
Sobyanin told reporters late Thursday that a residency check revealed that "two-thirds" of the worshippers at the city's main Cathedral Mosque were not registered in the city of Moscow.
"These are either people from the Moscow region or migrants without residency permits," he said in comments carried by Interfax.
Analysts and a prominent opposition leader said Friday that the comments were discriminatory and risked inciting renewed ethnic tensions.
Sobyanin said Thursday that "if only Muscovites came to the mosque, people who live here on a permanent basis and have residency status, there probably wouldn't be such a huge crowd."
In August, some 90,000 worshippers packed the streets around the Cathedral Mosque, near Olimpiisky Stadium, to mark the end of Ramadan.
Muslim leaders have long complained that Moscow, with just four mosques for an estimated 2 million worshippers, has a huge shortage of Muslim prayer houses. The Council of Muftis has demanded that a mosque be built in each of the city's 12 administrative districts.
But authorities have been quick to abandon plans to construct mosques following protests by locals.
Last month, City Hall announced that it was scrapping plans to build a large mosque in Mitino after 2,000 people gathered in the northwestern neighborhood to protest the mosque's construction.
Sergei Mitrokhin, leader of the liberal Yabloko party and a former City Duma deputy, said Sobyanin's argument was "weird" because the city's Christian churches were also used by nonresidents.
"Rather than formulating a policy for a multiconfessional city, he allows himself [to make] statements that can lead to interreligious tension," Mitrokhin told The Moscow Times.
Mitrokhin added that City Hall was "going along" with an Orthodox Church program of "mass construction of churches." He said local residents also felt provoked when churches were being built in "inappropriate" places, such as parks.
Olga Sibiryova, an analyst for the Sova think tank, said Sobyanin's statement is discriminatory because City Hall is not doing anything about protests of Orthodox church construction and because authorities are unlikely to conduct checks on the residency status of Christians.
"Ultimately, the lack of mosques might incite more tensions than the plans to build more," she said.