Four top NYPD commanders were removed from their supervisory posts Thursday amid a joint federal-city investigation into possible illegal payments of cash and gifts to high-ranking police officials by a pair of Brooklyn businessmen.

“This is not a particularity good day for the department,” Commissioner William Bratton said at a news conference.

Bratton said Deputy Chief Michael Harrington and Deputy Inspector James Grant had been placed on modified duty and transferred, and that Deputy Chief David Colon and Deputy Chief Eric Rodriguez had been transferred.

Grant and Harrington also were reportedly stripped of their weapons and badges.

The new nonoperational desk assignments for the four commanders affected by Thursday’s action by Bratton have yet to be determined, an NYPD spokesman said.

Harrington, a 30-year veteran, and Colon, a 24-year veteran, worked at the NYPD’s Housing Bureau in Brooklyn. Rodgriguez, also a 24-year veteran, supervised patrols in Brooklyn South. Grant, a 19-year veteran, worked at the 19th Precinct on Manhattan’s Upper East Side.

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Roy Richter, head of the captain’s union, said in a statement: “The allegations contained in media reports tarnish the unblemished records of those mentioned. . . . [I] hope the federal investigation is wrapped up quickly to allow them to defend their reputations in an open forum.”

None of the four have been charged with any crimes.

The probe has focused on allegations that police officials received tickets for sporting events, vacations, cash or jewelry, according to the officials, sources and various reports.

In a statement, Bratton said the potential violations under investigation included violations of NYPD rules and policies, New York City conflict-of-interest regulations and federal criminal law.

All four worked — at some point in their careers — out of the Brooklyn South borough command, including the 66th, 68th, 70th and 72nd precincts. This is an area with a large Orthodox Jewish population.

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Sources have said that the joint investigation is focusing on whether the two businessmen, prominent in the Orthodox Jewish community in that area of Brooklyn, gave police officials gifts in return for helping in their businesses or in their communities. The two businessmen also have ties to the de Blasio administration.

At an unrelated news conference on Wednesday, Mayor Bill de Blasio indicated that he might return campaign contributions from the businessmen after the inquiry’s findings are known.

The two businessmen have been identified as Jona Rechnitz and Jeremy Reichberg. An attorney for Rechnitz is reported to have said his client has done nothing illegal. Reichberg has not been reached for comment.

Some sources have said the initial investigation began as a look into the ties between the two businessmen and Philip Banks, the former top-ranking uniformed officer in the NYPD, and his close friend Larry Seabrook, the head of the city’s correction officers union.

Deputy Inspector James Grant has been stripped of his gun and badge. Photo Credit: NYPD

A dissident former official of the correction officers union has charged in a civil suit that Seabrook placed $5 million in a hedge fund in return for favors, such as paying for overseas trips.

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Seabrook has denied any improprieties, and Banks’ attorney, Benjamin Brafman, issued a statement Thursday denying his client has done anything wrong.

Officials attempted to minimize the extent of the investigation within the NYPD or how widespread the problem, if any, may be.

“We don’t believe this is deep, systematic corruption,” said NYPD Deputy Commissioner of Legal Matters Lawrence Byrne, who was present at a news conference with Bratton.

However, he would not comment on the scope of the investigation, or how many more police officials were believed to be involved.

NYPD Deputy Chief Eric Rodriguez, the second in command of Patrol Borough Brooklyn South, has been put on desk duty. Photo Credit: NYPD

Some of the police officers under scrutiny are suspected of engaging in a not uncommon, if frowned upon, practice in the department.

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“This is going to end a long-standing practice in the department,” said one source, noting that some brass and lower-level officers provide protection while off-duty for businessmen in some communities who are afraid of being robbed while transporting cash or jewelry.

The businessmen or community leaders also get the “benefit” of getting close to police to help with community issues such as parking problems and security at block parties. They also can simply like being associated with the police officers — the higher in rank the better, the sources said.

In one case, a police officer is suspected of receiving a “tip” of several hundred dollars to provide protection to a businessman transporting cash or jewelry, and assistance with a community issue, the sources said.

In another case under investigation, a person supposedly paid $200 for 200 Police Benevolent Association cards to a police official, the sources said. The cards, which are widely distributed gratis, are believed to help people get out of minor traffic tickets. Police union officials have denied this.

Police Commissioner William J. Bratton as he answers question about the FBI probing into the affairs of some high ranking police brass at the NYPD, during press conference at One Police Plaza in Manhattan. April 7, 2016. Photo Credit: John Roca

With William Murphy and Maria Alvarez