The provisions of this chapter shall not apply to vessels navigating under a certificate of enrollment under the control of a federally licensed pilot or to vessels otherwise exempt by the laws of the United States, or to vessels measuring less than one thousand (1,000) gross tons, and the draft of which, when fully loaded, would be less than twelve feet (12?) of water, other than vessels under registry. All vessels under registry are subject to the provisions of this chapter. If any vessel exempt from this chapter shall employ a pilot, the pilot shall be entitled to receive, as compensation for his or her services, pilotage fees in an amount not to exceed the rates established by the commission. Vessels are not subject to the provisions of this chapter if they receive special exemption from the commission where the commission determines that the vessels do not pose a threat to the environment.