A Manhattan court officer who refused to get the COVID-19 vaccine died of the virus on Tuesday, officials said.

Lt. Stephen Shyti, 63, who worked at Manhattan Criminal Court, died at a New York City hospital after battling the virus for over two weeks, Court Officers Union President Dennis Quirk confirmed.

Shyti, a familiar face at 100 Centre St., suffered medical conditions from working at Ground Zero and did not trust vaccines, Quirk said.

“He had some ailments from working numerous days and nights at the 9/11 site,” said Quirk. “He totally mistrusted the government and would not get the vaccine.”

But despite his stance on the vaccine, Quirk said Shyti always wore his mask while working.

“He was a great court officer and an even better person. Everyone he came into contact with liked and respected him,” said Quirk.

Office of Court Administration spokesman Lucian Chalfen said Shyti was beloved in the court system, having worked there for over two decades.

“Lt. Shyti was a 26 year veteran of the Court System who was a calm and reassuring presence at Manhattan Criminal Court,” Chalfen said. “He was well-liked by all members of his command and was known for his fairness and care for his co-workers.”

“He had an encyclopedic knowledge and grasp of all aspects of criminal court operations and case processing and was a resource for younger officers throughout his career,” Chalfen’s statement continued.

“He will be missed by his friends and colleagues, not only in the New York City Criminal Court where he spent the entirety of his career, but throughout the Unified Court System,” Chalfen said.

Shyti’s death comes as 52 percent of the court officers in the state have now been vaccinated, according to the most recent data provided to The Post by OCA.

Overall, 71 percent of the 15,6000 workers in the state’s court system have received the jab, said Chalfen.

There is currently no vaccine mandate for court workers, but one will reportedly take effect by the end of the month.

Chief Administrative Judge Lawrence Marks announced the upcoming mandate that would apply to all courthouse workers and go into effect on Sept. 27, according to an internal email obtained by The Queens Eagle.

Additional reporting by Priscilla DeGregory