N.Y. Comp. Codes R. & Regs. tit. 6, § 42.16
(2) All persons possessing a shellfish microbiological cleansing operator's permit or a shellfish microbiological cleansing-principal harvester's permit, pursuant to the provisions of this Part, must pay a supervision fee as specified below. Municipalities or other political subdivisions are exempt from the provisions of this section.
(b) Supervision fee and security requirements.
(4) The provisions of this subdivision shall not apply to political subdivisions of the State of New York.
(c) Fee schedule.
(g) The fees provided for above are the minimum fees which will be assessed by the department. In the event that the reasonable costs to the department of supervision over the removal of shellfish from uncertified areas exceed the minimum fee, additional fees sufficient to reimburse the department for such additional costs will be assessed monthly. Payment of the additional fee will be due within 15 days of the receipt of notice of its assessment. The additional fees shall be assessed as follows:
(a) Supervision.