Despite its constant financial woes, the MTA has been shelling out millions of dollars to flunky contractors that managers knew were doing lousy jobs.

Agency supervisors knowingly buried “F” grades for bad contractors just to keep them in the pool for future projects, according to a damning report released by the MTA Inspector General Tuesday.

“Literally billions of dollars are at stake,” MTA Inspector General Barry Kluger said.

Among the 40-pages of findings:

- The MTA doled out only 19 “unsatisfactory” reviews out of more than 2,500 performance evaluations issued to contractors between 2006 and 2008, which inspectors believe is far too low.

- MTA managers routinely scrapped unsatisfactory marks under pressure from agency bigwigs or because they hadn’t properly handled the paperwork.

— The MTA doesn’t check prior evaluations on its subcontractors even though they perform upwards of 70 percent of the agency’s major work.

- Long Island Rail Road was nine months tardy in recording poor marks for one contractor. In the meantime, three other MTA agencies gave the vendor almost $25 million in work.

“This is tough to defend. The new MTA chair needs to clean this up,” said Gene Russianoff, of the Straphangers Campaign.

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The mismanagement has gone on to this day, affecting everything from station upgrades to complex technology projects, inspectors found. Recent jobs include: Installation of elevators at the 168th street station for $6 million; new train supervision equipment for $147 million; and train countdown clocks for $131 million.

“There is a pervasive mindset, amounting to an institutional culture, to avoid unsatisfactory ratings,” Kluger said.

The MTA agreed to most of the report’s findings and pledged to adopt its recommendations, including cracking down on “delinquent” managers and conducting spot-checks on performance evaluations.

“Too often we have let our contractors slide,” MTA CEO Jay Walder said in a statement. “My top priority is changing how the MTA does business.”