The FBI put Gov. Kathy Hochul in her place after she labeled the federal probe into a Democratic Party boss a “political hit job” — as the feds revealed its agents are working jointly with state investigators.

Hochul had blasted an FBI investigation into Suffolk County Democratic Party Chairman Rich Schaffer even though she admitted to not knowing the particulars of the claims, brushing off the probe and bizarrely invoking President Trump.

But the federal law enforcement agency fired back at the Democratic governor on Tuesday, accusing her of playing politics ahead of Election Day on Nov. 3.

“It’s irresponsible to comment on joint state and federal investigations during the election campaign to score political points,” an FBI spokesperson told The Post. 

“It undermines the integrity of the investigative process and hurts the candidates running for office,” the spokesperson added. 

The rebuke is the agency’s first public confirmation of the probe and first acknowledgement that state investigators are working with the feds to look into the claims around Schaffer.

The Post first reported on the investigation, citing sources who had been interviewed by federal and state agents about the Dem boss. 

Schaffer, who has been the Suffolk party boss for over 26 years, was reelected to the top party post last month despite being hit with accusations that he tried to threaten party members and even offered money to some if they voted for him to keep the crown.

Hochul, asked about a federal probe into the accusations, pointed the finger at the Republican president even though the allegations against the Dem boss came from fellow party members.

“Anything coming out of the Trump administration days before an election… is calculated as a political hit job,” Hochul said earlier this month.

The Democrat is facing a reelection challenge from Republican Bruce Blakeman, who is no serving as the Nassau County executive.

Several party members and local government officials blew the whistle on Schaffer in September, saying he launched a Mafia-style pressure campaign for reelection just days before he defeated his progressive challenger Kathryn Casey Quigley in a battle for control of the party.

Quigley was his first challenger in his nearly 30 years in power. 

Schaffer has denied all allegations of wrongdoing and called them “baseless.”