They finally realized they were nuts.

New York officials issued a mea culpa on Friday for the seizure and slaughter of P’Nut the squirrel, a beloved pet. However, the delayed apology has left the grief-stricken owner still awaiting the return of the remains of his pet.

Amanda Lefton, the acting director of the state Department of Environmental Conservation, released a statement apologizing to New Yorkers for the harsh and insensitive treatment of the treasured pets, P’Nut the squirrel and Fred the raccoon, that occurred last fall.

“We know that we can do better moving forward,” Lefton said.

“We have carefully reviewed all public feedback and we understand the distress caused to communities throughout the state,” she added.

“I have made it a priority to conduct a review of our current wildlife protection and enforcement procedures to prevent similar incidents from happening in the future and to ensure the safety of New Yorkers and our agency,” Lefton stated.

The tardy remarks did not satisfy Mark Longo, P’Nut’s rescuer and owner, who told The Post the agency’s platitudes ring hollow.

“Today hurt me really bad. To be honest, I’m still shocked and really upset with the response,” he said in a statement.

“It took DEC almost five months to respond, and they respond with, ‘We can do better.’ Five months of not knowing why Peanut was killed. Five months, and we still don’t have the whereabouts of Peanut’s and Fred’s bodies.”

“No answers. There’s no remorse. I’m just at a loss,” Longo added.

As of December, the headless bodies of P’Nut and Fred were being preserved as evidence in a refrigerated room someplace upstate, a DEC spokesperson told The Post.

P’Nut and Fred were seized from Longo’s home by the DEC on Oct. 30 and euthanized by the agency one day later, after it received an anonymous complaint about an animal possibly infected with rabies at the Chemung County residence.

DEC agents combed through Longo’s house for hours — leaving with P’Nut and Fred, who the loving pet owner would never see again. Both of the animals had been rescued by Longo. 

The animal lover saved P’Nut, who was 6, from a New York City street after seeing the squirrel’s mother get struck by a car. Little P’Nut was just a baby at the time.

Fred was dropped at his doorstep, and he graciously took in the raccoon, who was about 4 months old when he was euthanized by DEC officials.

Lefton was named acting head of state DEC last month, replacing Interim Commissioner Sean Mahar, who was at the helm of the agency during the P’Nut fiasco.