A federal judge on Friday denied a request by Jewish organizations to temporarily block Governor Andrew Cuomo's order to restrict attendance at houses of worship as part of a renewed shutdown in regions of the state experiencing a surge in coronavirus cases.

"[The governor] has lawfully exercised his power without religious animus to make sure we don’t find ourselves back where we were in March," Judge Kiyo Matsumoto, of the federal district court in Brooklyn, referring to the period when New York became the epicenter of the pandemic.

Friday's ruling does not put an end to the lawsuit, but it means that the new round of hotspot restrictions can proceed as planned.

New York City began zoned shutdowns in portions of South Brooklyn and Queens on Thursday.

Under Cuomo's executive order, houses of worship in so-called "red zones" where the virus has been spreading fastest are not allowed to have more than 10 people in attendance. Aside from Brooklyn and Queens, the restrictions also apply to Binghamton and two suburban communities in Rockland and Orange counties.

Jewish groups, led by Agudath Israel, an umbrella organization for synagogues, argued that the limits on capacity amounted to a constitutional violation of religious freedom and that Cuomo had unfairly singled out the Orthodox community with his comments. The governor has repeatedly cited Orthodox communities for not complying with social distancing orders.

The state's new virus rules have also offended church goers. The Roman Catholic Diocese of Brooklyn have filed their own lawsuit.

The timing of the shutdown was significant, according to the plaintiffs. Friday marks the start of three major Jewish holidays—Hoshana Rabbah, Shemini Atzeret and Simhat Torah—during which tens of thousands of Orthodox individuals across the state are expected to gather for prayer, Torah readings and other rituals.

While sympathetic, Judge Matsumoto said she found the governor's order to be based on "sound medical and scientific evidence" of virus spikes in the state. She also said the shutdown was not any more restrictive of religious activities that secular ones. In fact, she said the opposite was true given that many non-essential businesses have been forced to close, and that in the most restricted zone, no mass gatherings are allowed. A federal judge in June had ruled that the state and city could not restrict religious gatherings while allowing Black Lives Matter protests.

Avi Shafren, a spokesman for Agudath Israel, expressed disappointment with Friday's decision but vowed to continue their legal battle.

“The game is not over, we intend to pursue whatever other options we have legal and otherwise, in order to preserve our right to live with reasonable health measures and we are encouraging all our congregations and affiliates to practice good health measures," he said.

The governor's office did not immediately return a request for comment.

But during a call with reporters on Friday, Cuomo denied that he was targeting the Orthodox community with his latest restrictions.

"This cluster happens to be predominantly the ultra-orthodox in Brooklyn and Queens. We have always attacked clusters," he said, adding, "Bars, restaurants, clusters, concert in the Hamptons - whenever there is a cluster, we have attacked it. So, this is nothing new."

With reporting from Gwynne Hogan.