Three high-ranking New York state troopers are set to retire Monday after the governor’s office took issue with their handling of an investigation into a workplace discrimination complaint, The Post has learned.

Cols. Pat Regan and Mary Clark and Lt. Col. Jim Michaels opted to resign rather than to be demoted to the rank of lieutenant, law enforcement sources said.

The trio of longtime troopers were given the ultimatum in connection to their probe into an Equal Employment Opportunity Commission complaint filed by a female trooper, according to the sources.

It was unclear what the complaint was over and when it was filed — but the governor’s office felt the case wasn’t being investigated quickly enough, a source said.

A law enforcement source said the shakeup was political in nature since Gov. Kathy Hochul is facing re-election.

“The governor doesn’t want any negative stories about how women are treated after the [Andrew] Cuomo allegations,” the source said, referring to the sexual harassment accusations against the disgraced former governor.

The departure of the three troopers is especially consequential since two of them are top-ranking colonels.

Regan is the deputy superintendent for field command and Clark is the deputy superintendent of labor relations and human resources.

The nature of their roles in the probe wasn’t immediately known.

“State Police learned about an internal complaint and that it was not handled properly and notified the Governor’s Office of Employee Relations to investigate further. We are reviewing our internal policies to ensure better processes and full compliance,” said director of public information Beau Duffy in a statement.

A spokesperson for the governor’s office didn’t immediately respond to a request for comment.

Regan, Clark and Michaels couldn’t be reached Sunday night.

Additional reporting by Bernadette Hogan