The veteran NYPD homicide detective who went missing on Thursday, sparking a massive manhunt, was found dead of an apparent suicide, police sources said.

The body of Joe Calabrese, 58, was found near bushes in Plumb Beach in Brooklyn Thursday afternoon, dead of an apparent self-inflicted gunshot wound to the head, police sources said.

“I don’t understand it. I don’t understand why he would do this,” said a stunned police officer who knew Calabrese.

The detective, who was assigned to the Brooklyn South homicide squad, was a longtime Detectives Endowment Association board member and union trustee.

“I am shocked and shattered beyond belief,” said Michael Palladino, president of the DEA. “Joseph Calabrese was a dedicated detective, union official, husband and father. He was the salt of the earth.”

Calabrese was last heard from around 2 a.m., after he left Maimonides Medical Center in Borough Park, where his wife had undergone a minor procedure, according to sources.

His black Cadillac sedan was found by another detective near the beach just off the Belt Parkway around 3 a.m., about five minutes from his home, sources said.

Calabrese didn’t report to work Thursday and was unreachable, a high-ranking police source said.

Earlier Thursday, at least 100 uniformed and plainclothes officers swarmed the parking lot of the Plumb Beach rest area where Calabrese’s Cadillac was parked.

Two men could be seen collapsing in the arms of detectives on the beach.

Calabrese’s death comes just a day after Steven Silks, the NYPD deputy chief of Queens North, fatally shot himself in the head Wednesday, while sitting in an unmarked patrol car. The 62-year-old chief had been weeks away from his scheduled mandatory retirement.

Additional reporting by Joe Marino