(a)(1) For taxable periods beginning on or after January 1, 2017, and before December 31, 2024, taxpayers that are granted amnesty and later fail to comply with any payment or filing provision administered by the department shall be subject to the penalty for underpayment due to negligence under subsection (c) of Section 40-2A-11, or a civil penalty of one hundred dollars ($100), whichever is greater.

(2) A taxpayer who delivers or discloses a false or fraudulent application, document, return, or other statement to the department in connection with an amnesty application is subject to the penalty for underpayment due to fraud under subsection (d) of Section 40-2A-11, or a civil penalty of ten thousand dollars ($10,000), whichever is greater.

(b) Following the termination of the tax amnesty period, if the commissioner issues a deficiency assessment for a period for which amnesty was taken, the commissioner may impose penalties and institute civil or criminal proceedings as authorized by law only with respect to the difference between the amount shown on the amnesty application and the correct amount of tax due. The commissioner may impose by rule, after the expiration of the tax amnesty period, a cost of collection penalty not to exceed twenty percent of any additional deficiency assessed for any taxable period for which amnesty was taken. This penalty shall be in addition to all other applicable penalties, fees, or costs. The commissioner may waive any or all of the collection penalty when it is demonstrated that any deficiency of the taxpayer was not due to negligence, intentional disregard of administrative rules, or fraud. The imposition of penalties or civil or criminal proceedings shall not invalidate the amnesty that was previously granted. No penalty shall be imposed if the deficiency results from an adjustment made by the Internal Revenue Service to the taxpayer's federal income tax and the taxpayer provides written notice of the adjustment to the commissioner within 60 days of receipt of the adjustment from the Internal Revenue Service or if the taxpayer's application for amnesty was based on a proposed assessment or notice of assessment.