An ethnic Tatar who formerly served as imam of the main Moscow mosque, he is perceived by some as a controversial figure. In early 1995, Abdul-Vakhid Niyazov, then chairman of the Islamic Cultural Fund of Russia and later a leading member of the Eurasian Party of Russia, accused Gainutdin of illegally dismissing two imams and treating visiting foreign Muslim dignitaries disrespectfully.

Gainutdin was criticized in the late 1990s for arguing for a more selective and precise use of the term "wahhabism." He alleged that the Russian authorities tend to use that term to denigrate any Muslim communities that they suspect of disloyalty to the Russian state.

He was in the news in April 2003 for responding to Tajetdin's call for jihad against the United States by saying such calls were "impermissible and dangerous" and while Muslims should help Iraq, they should not use unlawful means.