Sunday was the final day that religious groups could continue holding services in city schools.
Mayor Michael Bloomberg said Friday the city will begin enforcing a 2011 ruling by the Second Circuit Court of Appeals that found the city has the right to prohibit religious worship in schools.
The mayor cited the separation of church and state -- and the possibility that one religion could be favored over another -- for why the city is barring worship in public buildings.
"Someday the religion that the state picks as the 'state religion' might not be yours," Bloomberg said in his weekly radio address. "The way to solve that is to not have a state religion."
But some state lawmakers are pushing for legislation that would overturn the ban. Congregations typically pay rent or reimburse schools for the cost of holding services, and some said they'll be forced to pay more for outside rental space.