Two high ranking Bronx cops, a disgraced former NYPD transit boss and a deputy inspector, were transferred out of their precinct Thursday as probers look into allegations they filed phony time sheets.

Capt David Dent of the 45th Precinct, was stripped of his gun and badge and placed on desk duty for allegedly raking in cash when he was not working. He was transferred out of the precinct.

The precinct’s commander, Deputy Inspector Danielle Raia, was also transferred out on suspicion she was falsely clocking in at times, sources said. But she has not been placed on modified duty and has not yet been interviewed by the Internal Affairs Bureau.

The IAB probe was initiated at least two months ago, sources said.

In 2015, Dent allegedly tried to drive down his transit district’s crime numbers by bullying some victims to discourage them from filing police reports, sources told The Post at the time.

Roy Richter, president of the captains’ union, said of the current situation, “Dent is working through a family matter, which the department believes interferes with the high-caliber performance demanded of a captain.”

Another source said Dent had been telling people that he was skipping out on work to care for his terminally ill mother.