The prime contractor on the scandal-scarred CityTime municipal-payroll project yesterday coughed up nearly $2.5 million in salary paid to a former exec who falsified the number of hours he worked.

Science Applications International Corp. had promised to refund the money after Gerard Denault was busted last month for allegedly pocketing millions in kickbacks from a subcontractor.

Department of Investigation Commissioner Rose Gill Hearn noted: “The irony is that the time records of the top corporate manager of a multimillion-dollar project intended to modernize the city’s timekeeping system became the focus of a timekeeping investigation by his employer.”