Harbor Federal Credit Union is chartered under federal law. Federally chartered credit unions are regulated by the National Credit Union Administration (NCUA), an independent agency of the U.S. Government. NCUA's three board members are nominated by the President and confirmed by the Senate.

State chartered credit unions are regulated by their state credit union department. NCUA administers the federal insurance fund, NCUSIF, which covers all federal credit unions, and most state chartered credit unions. No taxpayer money is used for regulating and overseeing federal credit unions, as all activities of NCUA and the NCUSIF are funded by credit unions.