The state police union has issued a scathing report calling for an overhaul of State Police leadership and accusing the department of a “two-tier system of employee discipline.”

The report was sent to Governor Spitzer last week on the anniversary of the shooting of three state troopers last year. It accused the state police department’s investigation into the manhunt for Ralph Phillips — who shot three troopers, killing one of them — of being a sham that protected the top brass. The report was first published on the Daily News Web site yesterday.

“There is a wide belief that State Police members of the highest ranks are ‘taken care of’ when faced with Discipline,” the report said.

The report follows accusations by the state attorney general that Governor Spitzer’s staff inappropriately worked with top State Police officials in a campaign against Senate majority leader, Joseph Bruno. Much of the report’s ire is directed at officials appointed under Governor Pataki, many of whom have since resigned.

A spokesman for Governor Spitzer, Paul Larrabbee, said the governor’s office was reviewing the report.