City officials have given out 62 fines totaling $US150,000 ($A207,000) for violations of COVID-19 rules in hot spots in Brooklyn and Queens over the weekend.
Five unnamed religious institutions were among those hit.
The crackdown came amid an alarming spike in COVID-19 cases from Borough Park, Brooklyn, to Kew Gardens, Queens.
With many of the affected areas home to large Orthodox Jewish populations, leaders have pleaded with the communities to shy away from large gatherings.
Last week, Mayor Bill de Blasio announced fines of up to $US15,000 dollars for holding big get-togethers and up to $US1000 dollars for those who refuse to wear face coverings.
Under new state rules, houses of worship in the hot spots haven't been allowed to host groups of more than 10 since last Thursday.
"To keep all of New York City safe, we must work together," read a Sunday afternoon message from the city government's Twitter account.
"The recent COVID outbreaks in Brooklyn and Queens will continue to receive additional FREE resources and strong enforcement."
Earlier on Sunday, Governor Andrew Cuomo faulted the city for failing to enforce COVID-19 rules.
"People see that a law isn't enforced - they dismiss the law," he told reporters.