Acknowledging that New York's restrictions "do seem unduly restrictive", Roberts pointed out that Governor Cuomo revised his restrictions to depart from a strict numerical limit on religious gatherings, and instead, allow a 50% capacity cap.
The justices split 5-4 to bar the state from enforcing the restrictions against the groups for now, with new Justice Amy Coney Barrett in the majority.
Justice Neil Gorsuch penned his own concurrence to the per curium order, saying, "Government is not free to disregard the First Amendment in times of crisis".
Chief Justice John Roberts joined with the court's three liberal justices, Sonia Sotomayor, Elena Kagan and Stephen Breyer in arguing that the governor's zone restrictions on religious gatherings are constitutional. Earlier this year, it had turned away similar requests by churches in Nevada and California with a 5-4 majority decision leaning liberal prior to the death of Justice Ruth Bader Ginsberg.
The justices acted on an emergency basis while lawsuits challenging the restrictions continued.More news: 'Final warning' for Pakistan cricketers in New Zealand
The court ruled 5-4 to bar Cuomo from enforcing his October 6 "Cluster Initiative" against houses of worship that sued to challenge the restrictions. Noting that New York's restrictions are tighter than those of other states, Kavanaugh said those rules "not only are severe, but also are discriminatory".
The groups are now subject to less-restrictive rules because they're now in areas designated yellow zones.
Andrew Cuomo, governor of NY state, had ordered that only up to 10 people could gather at sites of worship in high-risk areas designated "red zones". The majority said his limits violated the First Amendment's protection of the free exercise of religion.
The Orthodox congregations Agudath Israel of Kew Garden Hills and Agudath Israel of Madison, as well as nationwide Orthodox Jewish group Agudath Israel of America.
They said Cuomo's orders were not "neutral" toward religion, but "single out houses of worship for especially harsh treatment".More news: Photos of packed USA airports show how Americans are defying CDC guidance
Gorsuch said the governor's order deemed many retail businesses an essential, including hardware stores, liquor stores and bike fix shops. In the "orange zones", as many as 25 may attend.
Leaders of Agudath Israel, an organization that represents Haredi Orthodox Jews across the country, said the orange and red zone restrictions were needlessly broad.
"Governor has chosen to impose no capacity restrictions on certain businesses he considers 'essential, '" commented Gorsuch, "And it turns out the businesses the Governor considers essential include hardware stores, acupuncturists, and liquor stores".
New York, for its part, told the court that religious gatherings were being treated less restrictively than secular gatherings that carried the same infection risk, like concerts and theatrical performances, which were prohibited entirely.
"Even in a pandemic, the Constitution can not be put away and forgotten", read the opinion, which sided with a petition brought forth by NY religious organizations.More news: Amazon AWS fault is taking down parts of the internet
A federal judge in Brooklyn rejected separate requests made by the religious groups on October 9.