After days of discord over how to address rising coronavirus cases in Orthodox Jewish areas, Gov. Andrew M. Cuomo on Tuesday imposed tough new restrictions on parts of New York City and its northern suburbs that would have an especially pronounced impact on synagogues and other houses of worship.

Mr. Cuomo also detailed an array of new rules that would shut down schools, restaurants, bars and gyms in portions of Brooklyn and Queens, as well as in Rockland and Orange Counties and in Binghamton.

Mr. Cuomo’s order was intended to end confusion over how the state and city government would address the spreading outbreak in neighborhoods with large populations of Orthodox Jews, some of whom have flouted limits on gatherings, officials say. On Sunday, Mayor Bill de Blasio proposed that schools and nonessential businesses in nine ZIP codes in New York City be shut down to curb the virus.

A day later, Mr. Cuomo said he would not approve the mayor’s plan, indicating that he would offer his own that used different geographic criteria, and noting that the mayor had not mentioned religious institutions. On Tuesday, in announcing his actions, Mr. Cuomo explicitly singled out houses of worship for new capacity limits, and prohibited mass gatherings in certain areas where there are virus clusters.

“This is about mass gatherings,” he said. “And one of the prime places of mass gatherings are houses of worship.”

The governor added that schools in parts of Rockland and Orange Counties would also close, a day after he made the same declaration for schools in parts of Brooklyn and Queens.

The fresh set of lockdown measures — which Mr. Cuomo, not Mr. de Blasio, has the authority to impose — are a somber setback for New York, once the epicenter of the pandemic. Officials had managed to keep the virus in check over the summer, but only after it had led to the deaths of tens of thousands of people.

But the virus has returned in specific pockets of the state: In the 20 ZIP codes that Mr. Cuomo deemed most problematic, the positivity rate was 5.5 percent on Tuesday, far exceeding the 1.2 percent rate for the rest of the state.

The urgency behind the news conference in the State Capitol, Mr. Cuomo’s first briefing in Albany in months, harked back to the early days of the pandemic when he began sharing updates on the state’s first cluster in New Rochelle, N.Y., in Westchester County, where dozens of members of a synagogue became infected in March.

The new rules, which will be in place for at least two weeks, may go into effect as soon as Wednesday, but no later than Friday, Mr. Cuomo said.

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Cuomo Imposes New Restrictions to Curb Coronavirus Clusters

Gov. Andrew M. Cuomo announced tighter restrictions on Tuesday aimed at curbing the surge in coronavirus clusters in parts of New York City and some suburbs.

The virus spreads in mass gatherings. We know this from our own experience, from what we’ve seen and from what every expert tells us, right? The outbreaks, which is when the virus is spreading out of control, it starts with a mass gathering and then it expands from there, especially indoors. So it’s to be taken very seriously. A mass gathering causes infections, infections cause a cluster, a cluster causes community spread. That is the natural evolution of things unless we intervene and we stop the cycle. What’s our strategy? Crush the cluster and stop the spread. And we’re announcing a special initiative to do just that — Cluster Action Initiative. Catchy name. Step 1, you take the most dramatic action within the cluster itself, where you have the highest density of cases. Understanding that the people in that cluster interface with the surrounding communities, take additional action in the communities surrounding the cluster. And then on a precautionary measure, take action in the communities that are outlying that area, right? So three steps.

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Gov. Andrew M. Cuomo announced tighter restrictions on Tuesday aimed at curbing the surge in coronavirus clusters in parts of New York City and some suburbs.CreditCredit…Mike Segar/Reuters

“A mass gathering causes infections, infections cause a cluster, a cluster causes community spread,” said Mr. Cuomo, a third-term Democrat. “That is the natural evolution of things unless we intervene and we stop the cycle.”

Even so, Mr. Cuomo — who has ridden his handling of the coronavirus crisis to high popularity ratings and an enhanced national profile — seemed vexed that the virus had once again gained a foothold in his state.

“If we had enforced the laws we would not be here today,” Mr. Cuomo said, blaming localities for not enforcing social distancing rules and mask mandates. He added that the gatherings that he believed caused the spike in infections “were all illegal.”

The reintroduction of restrictions on houses of worship caught religious leaders in Brooklyn and Queens by surprise, and many expressed frustration at both the decision and the process by which it was made.

“All of this seems very poorly executed, the decision and the communication, all of it,” said Rabbi Motti Seligson, a spokesman for the Chabad-Lubavitch Hasidic movement, which is based in Brooklyn and is one of the largest Jewish organizations in the world.

“The rhetoric from public officials sound very punitive and that usually means they feel like they have lost control,” Rabbi Seligson said. “And that is not a good place to be in, for anyone who lives in these areas.”

Bill Neidhardt, a spokesman for Mr. de Blasio, said City Hall was still reviewing the governor’s new restrictions, including the limits on houses of worship.

“What is really important for us is that what we put forward protects the health of all New Yorkers,” he said.

The new restrictions were divided into three color-coded zones — red, orange and yellow — each with different rules for gatherings, schools and businesses.

Restaurants in a red zone, for example, will be limited to takeout only, while eateries in an orange zone will be limited to outdoor dining and four people per table. Houses of worship in a red zone will be limited to 25 percent capacity or a maximum of 10 people, while those in a yellow zone would remain capped at 50 percent capacity.

Only essential businesses are allowed to remain open in a red zone, while all businesses will be allowed to operate in a yellow zone.

The exact boundaries of all the new cluster zones began to emerge late Tuesday, with Mr. Cuomo posting on Twitter a map of the Brooklyn cluster zone, which appeared to include the neighborhoods of Bay Ridge, Borough Park, Midwood, Sheepshead Bay and Sunset Park, and maps for the other cluster zones.

But in asserting control over the situation, Mr. Cuomo may have sown further questions. The tiered system of restrictions, for example, could lead to confusion among business owners who operate on the same street, but are bound by different rules.

A large part of the disagreement between the governor and the mayor revolved around how to delineate where the new restrictions should be applied.

The mayor had said he preferred closing businesses based on their ZIP codes, which he said people were more familiar with and which could cover a broader swath of the area.

“If you are restricting in the places that are really, really the toughest, you also want restrictions in the immediate surrounding perimeter and that’s why the ZIP code model, actually the more I looked at it, the more sense it made,” Mr. de Blasio said on Tuesday before the governor’s announcement. “It was a way to stop the spread from going into more and more neighborhoods.”

But the governor argued that ZIP codes, which are used to sort mail and are not technically geographic boundaries, could lead to arbitrary zones that did not capture where infection rates were actually rising.

Whatever the method used to draw the lines, Mr. de Blasio had publicly pressured Mr. Cuomo to take “quick and decisive” action on the issue, saying he would abide by the governor’s plan.

“I said, ‘Look, here is what I propose. This would work. We all understand what a ZIP code is. This would work. Let’s go. We have to act decisively,’” Mr. de Blasio said before Mr. Cuomo’s announcement. “If they have a different model, it’s their call and we’ll work with whatever model they choose, but we have to move quickly.”

The deadline for such rules to be enacted is Friday, a three-day window that the governor said was necessary to get the word out to communities, even as the virus seemed to be spreading.

“I would like to see them do it tomorrow, ” the governor said, noting that it would be up to localities to inform businesses and houses of worship of new restrictions. “So they know what the rule is, so they can follow the rule.”

Over the last week, the statewide rate of infection has regularly topped one percent — it was 1.45 percent in tests reported to the state on Monday — reflective of much higher rates of infection in hot spots.

Mr. de Blasio and Mr. Cuomo have repeatedly voiced warnings as cases spiked in other states, and schools and workplaces reopened in New York. And on Tuesday, Mr. Cuomo struck an almost resigned tone about an autumn resurgence of cases. “The leaves come down,” he said, “The virus goes up.”

Still, the dissonance between the two leaders — both Democrats, engaged in a long, internecine political feud — has caused confusion and consternation for residents of the hot spots, as well as for other elected officials, wary of its impact on the city’s response to a possible second wave.

Jumaane Williams, the New York City public advocate, said the “back and forth” between Mr. Cuomo and Mr. de Blasio was reminiscent of disputes between the two men in March, during the early days of the pandemic, “when delays and power plays led to lives lost.”

“Since then, the only thing that has been consistent between them is inconsistency,” Mr. Williams, a Democrat, said in a statement on Monday.

Jesse McKinley reported from Albany, N.Y. Liam Stack contributed reporting from New York.