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The Roman Catholic Diocese of Brooklyn is turning to the Supreme Court over coronavirus restrictions that New York Gov. Andrew Cuomo imposed that include limits on how many congregants can gather for religious services.

The emergency court filing, submitted Thursday, compares the prohibitions houses of worship face with the relative freedom afforded to many businesses under an order that Cuomo issued in October, in which he designated color-coded zones with varying degrees of limitations.

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“While this Executive Order effectively closes churches and other houses of worship, all businesses deemed 'essential' by the Governor—including everything from supermarkets to pet stores, huge hardware stores to brokers' offices—are permitted to remain open without any capacity limitations whatsoever, even in the most restrictive 'red' zones. In 'orange' zones, even the vast majority of nonessential businesses, including department stores, can remain open without limitation—yet churches cannot,” the filing said.

Cuomo’s order limited services at houses of worship to no more than 10 people in red zones, regardless of the size of the building, with orange zones capped at 25 and yellow zones at 50% capacity.

The diocese claimed that they were hit with these restrictions even though they themselves had not seen any spike in COVID-19 cases, while businesses deemed “essential,” such as grocery stores, large hardware stores and pet stores were unaffected in red zones, and more businesses enjoyed freedom in other zones without restrictions on capacity. They alleged that such a difference in treatment violated the Free Exercise Clause of the First Amendment.

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“Absent relief on an as-applied basis, thousands of the Diocese’s parishioners in Brooklyn and Queens will continue to be deprived of their core Free Exercise rights on a daily basis until the matter is resolved in the lower courts,” the filing said, “even though it is undisputed that the Diocese has complied with all prior health regulations and operated safely without any COVID-19 spread since being permitted to reopen several months ago.”

A lower court had previously ruled against the diocese.

The various zones in New York City are also home to large Orthodox Jewish populations. The order prompted outcries and protests from members of some of those communities, claiming that they amounted to anti-Semitic discrimination after New York City Mayor Bill de Blasio had singled out the city’s Jewish community for large gatherings that violated restrictions, while not doing the same in response to gatherings by other populations.

This week, Cuomo announced new restrictions in response to a recent spike in COVID-19 cases. As of Friday night, bars and restaurants with liquor licenses in the state must close at 10 p.m., as will gyms. Indoor gatherings -- even in private homes -- will be capped at 10 people.

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Cuomo also urged residents to wear masks, get tested and follow coronavirus-related health guidelines.

“Take this seriously,” he said.

Fox News' Michael Ruiz contributed to this report.