NAO also found the inspectorate's prosecution of pollution offenders to be very uneven, with penalties varying substantially from area to area.

According to a pollution scorecard released by the Environmental Defense Fund, the Port Jefferson plant is the third-worst air pollution offender on Long Island and ranks in the top 20 percent in the United States for carbon monoxide emissions.

In the last five years, the agency said 1,800 sewage spills resulted in thousands of gallons of sewage discharged into the bays and lagoons, making San Diego the worst pollution offender in California and one of the worst in the country.