(a) In determining the annual program fee the department will rely upon the number of vehicles listed on the waste transporter permit filed pursuant to title 3 of article 27 of the ECL. The fee will be prorated for vehicles issued permits for less than a full year. Nothing in this section shall prevent the department from determining a fee based upon the actual number of vehicles used by a transporter to transport regulated waste if it is more than the number of vehicles listed on the permit.