The city’s police watchdog is investigating the NYPD over its call not to arrest Daniel Penny in the chokehold death of Jordan Neely on the subway last week, The Post has learned.

A spokeswoman for Civilian Complaint Review Board confirmed Thursday that a complaint had been filed with the agency and a formal probe was under way to see if there was any wrongdoing in the decision not to charge Penny, 24, after he was questioned by cops following Neely’s death on May 1.

It’s unclear who filed the complaint.

Penny’s release sparked backlash, with protesters and lawmakers calling for his arrest. He’s now set to turn himself in to cops Friday to face a second-degree manslaughter charge.

The CCRB would see if there was evidence of misconduct by the officers or supervisors involved in the decision to release Penny without charges. No such evidence has emerged.

The agency recently substantiated a complaint that NYPD Chief of Department Jeff Maddrey abused his authority by ordering a Brooklyn precinct sergeant to void the arrest of an ex-cop accused of flashing a gun at three teens in 2021.

Maddrey could face a maximum punishment of 10 docked vacation days on the misconduct charge.

A spokesperson for the department did not respond to a request for comment Thursday.

Chief of Detectives James Essig told reporters on Wednesday that the department was “actively” working with the Manhattan District Attorney’s Office on the case.

“We have to methodically go through all my evidence with them [Manhattan DA], interview all witnesses, that was a pretty crowded train,” Essig said.

He did not answer any specifics about how many witnesses or who was interviewed, citing the ongoing investigation.

Police officials initially said cops had taken Penny into custody following the incident on a northbound F train in lower Manhattan, but by the next morning, it became public that they had let him go without charges.

Within a day, a video surfaced capturing the former Marine putting the 30-year-old homeless man in the fatal headlock and the city Medical Examiner’s Office had ruled Neely’s death a homicide due to compression of the neck.

NYC subway choking victim Jordan Neely: What we know

When: May 1, 2023

Who: Jordan Neely, 30, a homeless man was fatally strangled aboard a northbound F train just before
2:30 p.m., according to police.

He reportedly started acting erratically on the train and harassing other passengers before being
restrained and ultimately choked by a straphanger, identified as a 24-year-old marine from Queens.

The marine, who was seen on video applying the chokehold, was taken into custody and later released
but the DA is mulling charges, which could include involuntary manslaughter, according to experts.

Fallout: The city medical examiner ruled Neely’s death a homicide, noting he died due to “compression
of neck (chokehold).” This will be weighed during the investigation into whether charges will be brought
for Neely’s death.

Neely’s aunt told The Post that he became a “complete mess” following the brutal murder of his mother
in 2007. She noted he was schizophrenic while suffering from PTSD and depression.

“The whole system just failed him. He fell through the cracks of the system,” Carolyn Neely said.

Law enforcement sources said Neely had “numerous” arrests on his record, including for drugs,
disorderly conduct, and fare beating.

At the time of his death, Neely had a warrant out for his arrest for a November 2021 case where he was
accused of assaulting a 67-year-old woman in the East Village, the sources said.

Mayor Eric Adams has said it’s important for the DA to complete the investigation into Neely’s death and
not rush to conclusions.

The DA’s office had been investigating whether to pursue charges.

Penny’s attorneys have said he didn’t intend to kill Neely when he put him in a chokehold as the troubled man was going on a threatening rant aboard the train.

The lawyers didn’t return requests for comment Thursday.