Nine employees object on religious grounds, and the lead plaintiff in the lawsuit is Michael Kane, a special education teacher seeking religious exemption after he was denied.
Kane says the exemption process carried out by the city was "improper" and "discriminatory."
The three-judge panel of the 2nd US Circuit Court of Appeals, however, seemed unlikely to halt the vaccine mandate.
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While Judge Pierre Laval conceded they may have valid points he said the city does too.
"The city has a very, very strong interest in protecting school children from COVID," Laval said during oral arguments.
The judges seemed wary of stopping a mandate that 96% of DOE employees have already followed in favor of nine people.
"Discrimination is ongoing," said Sujata Gibson, who represents the employees.
An attorney for the city, Susan Paulson, said the mandate does not discriminate because it applies to every religion, political persuasion and background.
"The mandate is not substantially under-inclusive," Paulson said. "It's facially neutral."
The 2nd Circuit recently lifted an injunction on New York State's vaccine mandate for health workers.
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