The secretary shall make a final decision on a permit application within 240 days of the receipt of the application unless the time for such decision has been extended by the applicant in writing or by rules and regulations adopted by the secretary for the issuance of permits under this act. In the issuance of such permits, the secretary may include conditions specifically applicable to the operation of the facility. No local ordinance, permit or other requirements may prohibit operation of a facility having a permit under this act.