"The notion that people gather in large numbers and even if they didn't mean to would spread a disease that will kill other members of the community is just unacceptable to me," he said.
NYPD Commissioner Dermot Shea added police officers are also put at risk by such large gatherings.
The mayor said the city will no longer tolerate these kinds of gatherings in any community.
The funeral for Rabbi Chaim Mertz, who reportedly died from coronavirus complications, took place outside of a synagogue on Bedford Avenue in the Brooklyn community on Tuesday night.
There was no one inside the building, but when the procession happened hundreds of mourners took to the streets.
Many wore masks and masks were being handed out, but many were not masked.
The large gathering is a direct violation of the governor's executive order for social distancing.
NYPD was on the scene. Until now, they have taken the position that they are here to educate. Mayor de Blasio changed the approach after seeing what was happening.
He tweeted that he went to the scene himself and saying his "message to the Jewish community, and all communities, is this simple: the time for warnings has passed. I have instructed the NYPD to proceed immediately to summons or even arrest those who gather in large groups. This is about stopping this disease and saving lives."
That tweet unleashing a slew of backlash.
Critics accused de Blasio of singling out the Orthodox Jewish community for censure when others have violated social distancing rules as well.
"This has to be a joke," City Councilman Chaim Deutsch, who represents a large Orthodox Jewish constituency, tweeted.
Jonathan Greenblatt , CEO of the anti- defamation league, tweeted, "There are 1mil+ Jewish people in #NYC. The few who don't social distance should be called out - but generalizing against the whole population is outrageous especially when so many are scapegoating Jews."
The mayor responded on Wednesday, saying "If in my emotion I said something that in any way was hurtful, I'm sorry about that. That was not my intention. But I also want to be clear - I have no regrets about calling out this danger and saying I want to deal with it very, very aggressively."
There were no arrests, but Commissioner Shea said a dozen summonses were issued citing social distancing violations and refusal to disperse.
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