§ 688. Interest on overpayment.–(a) General.–Notwithstanding the provisions of § 16 of the state finance law, interest shall be allowed and paid as follows at the overpayment rate set by the commissioner pursuant to section six hundred ninety-seven, or if no rate is set, at the rate of six per cent per annum upon any overpayment in respect of the tax imposed by this article:

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(1) from the date of the overpayment to the due date of an amount against which a credit is taken;

(2) from the date of the overpayment to a date (to be determined by the commissioner) preceding the date of a refund check by not more than thirty days, whether or not such refund check is accepted by the taxpayer after tender of such check to the taxpayer. The acceptance of such check shall be without prejudice to any right of the taxpayer to claim any additional overpayment and interest thereon.

(3) Late returns. Notwithstanding the provisions of paragraph one or two of this subsection, in the case of a return of tax which is filed after the last date prescribed for filing such return (determined with regard to extensions), no interest shall be allowed or paid for any day before the date on which the return is filed.

(4) Interest on certain refunds. To the extent provided for in regulations promulgated by the commissioner of taxation and finance, if an item of income, gain, loss, deduction or credit is changed from the taxable year or period in which it is reported to the taxable year or period in which it belongs and the change results in an underpayment in a taxable year or period and an overpayment in some other taxable year or period, the provisions of paragraph three of this subsection with respect to an overpayment shall not be applicable to the extent that the limitation in such paragraph on the right to interest would result in a taxpayer not being allowed interest for a length of time with respect to an overpayment while being required to pay interest on an equivalent amount of the related underpayment. However, this paragraph shall not be construed as limiting or mitigating the effect of any statute of limitations or any other provision of law relating to the authority of such commissioner to issue a notice of deficiency or to allow a credit or refund on an overpayment.

(5) Amounts of less than five dollars. No interest shall be allowed or paid if the amount thereof is less than five dollars.

(b) Advance payment of tax, payment of estimated tax, and credit for income tax withholding.–The provisions of subsections (h) and (i) of section six hundred eighty-seven applicable in determining the date of payment of tax for purposes of determining the period of limitations on credit or refund, shall be applicable in determining the date of payment for purposes of this section.

(c) Income tax refund within forty-five days of claim for overpayment.–If any overpayment of tax imposed by this article is credited or refunded within forty-five days after the last date prescribed (or permitted by extension of time) for filing the return of such tax on which such overpayment was claimed or within forty-five days after such return was filed, whichever is later, or within six months after a demand is filed pursuant to paragraph six of subsection (b) of section six hundred fifty-one of this chapter, no interest shall be allowed under this section on any such overpayment. In regard to an amended return claiming such overpayment or a claim for credit or refund on which such overpayment was claimed, if such overpayment is refunded within forty-five days of filing such return or such claim, no interest shall be allowed from the date such return or such claim is filed until the day the refund is made. For purposes of this subsection, any amended return or claim for credit or refund filed before the last day prescribed (or permitted by extension of time) for the filing of the return of tax for such year shall be considered as filed on such last day.

(d) Refund of income tax caused by carryback.–For purposes of this section, if any overpayment of tax imposed by this article results from a carryback of a net operating loss, such overpayment shall be deemed not to have been made prior to the filing date for the taxable year in which such net operating loss arises. Such filing date shall be determined without regard to extensions of time to file. For purposes of subsection (c) of this section any overpayment described herein shall be treated as an overpayment for the loss year and such subsection shall be applied with respect to such overpayment by treating the return for the loss year as not filed before claim for such overpayment is filed. The term "loss year" means the taxable year in which such loss arises.

(e) No interest until return in processible form.

(1) For purposes of subsections (a) and (c) of this section, a return shall not be treated as filed until it is filed in processible form.

(2) For purposes of paragraph one of this subsection, a return is in a processible form if–

(A) such return is filed on a permitted form, and

(B) such return contains–

(i) the taxpayer's name, address, and identifying number and the required signatures, and

(ii) sufficient required information (whether on the return or on required attachments) to permit the mathematical verification of tax liability shown on the return.

(f) Overpayment credited against past-due support, or against a past-due legally enforceable debt, or a city of New York tax warrant judgment debt, or defaulted guaranteed student, state university or city university loans.–If interest is payable pursuant to this section on that portion of an overpayment of tax imposed by this article which is certified by the commissioner of taxation and finance to the comptroller as the amount to be credited against past-due support, or against a past-due legally enforceable debt, or a city of New York tax warrant judgment debt, or the amount of a default in repayment of a guaranteed student, state university or city university loan, as the case may be, pursuant to the provisions of section one hundred seventy-one-c, section one hundred seventy-one-d, section one hundred seventy-one-e, section one hundred seventy-one-f or section one hundred seventy-one-l of this chapter, such portion of such an overpayment shall cease to bear interest on the date of such certification.

(g) Cross-reference.–For provision with respect to interest after failure to file notice of federal change under section six hundred fifty-nine, see subsection (c) of section six hundred eighty-seven.

(h) Notwithstanding any other provisions in this section, for taxable years beginning on or after January first, two thousand eight and before January first, two thousand nine, interest will be allowed on an overpayment on any return or report on which one or more empire zone tax credits are claimed, only from the one hundred eightieth day after the taxpayer files with the department an empire zone retention certificate issued pursuant to subdivision (w) of § 959 of the general municipal law to the empire zone enterprise which is the basis for the tax credit or credits claimed on the return or report.