The department shall not charge permit fees for:

(1) Permits issued by a city, town, or municipal corporation under RCW 90.48.165;

(2) Permits issued by the energy facilities site evaluation council under RCW 80.50.071;

(3) Permits administered by the EPA under 33 U.S.C. 1251 et seq.

Nothing herein shall restrict the department from charging fees to recover administrative expenses of permits it issues under RCW 90.48.160 for discharges into municipal sewer systems, nor for charging fees to recover administrative expenses related to monitoring compliance with delegated pretreatment programs.