BOSTON — The company that once managed Massachusetts Bay Transportation Authority parking lots has agreed to pay $5.6 million to settle allegations that its employees skimmed millions of dollars from the transit agency.

Attorney General Maura Healey said Monday that LAZ Parking Limited LLC has agreed to pay $1.1 million to the state to resolve allegations that it failed to implement proper revenue controls and auditing tools at 13 MBTA lots.

LAZ has also agreed to pay $4.5 million to settle a lawsuit filed by the MBTA alleging breach of contract.

Healey says the thefts robbed the public of finds needed to invest in transportation.

LAZ’s contract was terminated March 31.

LAZ in a statement blamed the thefts on three “dishonest” employees and said the company has “accepted our share of any responsibility.”

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