Conn. Gen. Stat. § 12-39g

(b) For purposes of subsection (a) of this section, any taxes for general or special purposes levied by a municipality, any taxes imposed under chapter 223 and payable to such municipality, any fines, penalties, costs or fees payable to such municipality for the violation of any lawful regulation or ordinance in furtherance of any general powers as enumerated in section 7-148 , or any charge payable to such municipality for connection with or for the use of a waterworks or sewerage system shall be treated as if they were taxes due to the state, where, pursuant to section 12-2 , an agreement exists between the commissioner and the governing authority of such municipality providing for the collection by the commissioner, on behalf of such municipality, of such taxes, fines, penalties, costs or fees, or charges, provided such taxes, fines, penalties, costs or fees, or charges are (1) unpaid and a period in excess of thirty days has elapsed following the date on which they were due and (2) not the subject of a timely filed administrative appeal or of a timely filed appeal pending before any court of competent jurisdiction.

Section creates a mandatory, as opposed to directory, obligation on the part of the comptroller either to reduce a payment to a person by the amount of taxes owed by such person or to not issue a payment at all. 332 C. 776.