A Brooklyn suspect with 56 prior arrests escaped from police custody Tuesday — with his hands still cuffed behind his back — enraging the city’s top cop.

It was at least the fifth time since June that a suspect has escaped NYPD custody.

“Once again, an embarrassment for the department and something that we will deal with very severely as far as the officers involved,” ­Police Commissioner Bill Bratton fumed to reporters.

“[The officers] are an embarrassment to themselves in terms of their professional skills, or lack of them, in once again letting a prisoner escape in this city, and they will be dealt with very appropriately for that incompetence.

“I’m getting tired of it, as is the chief,” Bratton said.

“I’m very concerned when somebody with a pair of handcuffs, handcuffed behind them, can flee from three of my officers and they can’t catch him. I’m sorry — there’s something wrong there when that’s happening, repeatedly, over and over again.”

Gerald Brooks, 39, escaped shortly after two investigators and a sergeant from the Brooklyn South Warrant Squad cuffed him at a building on Sheffield Avenue near New Lots Avenue in East New York at about 5:30 a.m. sources said.

They were picking him up on a warrant for driving without a license — but also wanted to question him about five separate domestic-violence incidents, cops said.

As one of the officers was escorting Brooks into a police van, the prisoner shoved him and made a run for it ­before the cops lost sight of him.

NYPD Chief of Department James O’Neill said that he knows the sergeant involved in the case and that the cop is humiliated.

“He’s been in the Warrant Squad for a long time. He’s put hundreds of very dangerous people in jail,” O’Neill said. “So what happened to him this morning and the two other investigators involved, I’m sure . . . All three of them were ­absolutely embarrassed.”

O’Neill said it’s unclear how many of the cops actually had their hands on Brooks when he broke free.

“The perp was able to push away from the investigator and was able to run down the street,” O’Neill said.

The majority of Brooks’ arrests are domestic, but O’Neill said the suspect also has racked up several other charges such as for assault.

“You name it, he’s got it,” O’Neill said. “This is a guy that’s a problem. This is who I want the Warrant Squad to go out and get. But, you know, they need to hold onto him.”

“You name it, he’s got it,” O’Neill said. “This is a guy that’s a problem. This is who I want the warrant squad to go out and get. But, you know, they need to hold onto him.”

Suspects who have escaped custody in the past range from Tiffany Neumann, who slipped away from cops who were supposed to be guarding her as she was being treated at a lower Manhattan hospital after a shoplifting arrest in ­August, to career criminal Tareek Arnold, 23, who shoved an officer in June and ran off with his hands bound behind his back. It took cops more than a month to catch him.

Additional reporting by Daniel Prendergast