(1) If the tax commission determines that any amount due under this chapter has been paid more than once or has been erroneously or illegally collected or computed, the commission shall set forth that fact in its records and the excess amount paid or collected may be credited on any amount then due and payable to the commission from that person and any balance refunded to the person by whom it was paid or to his successors, administrators or executors. The tax commission is authorized and the state board of tax appeals is authorized to order the tax commission in proper cases to credit or refund such amounts whether or not such payments have been made under protest and certify such refund to the state board of examiners.
(2)  No such credit or refund shall be allowed or made after three (3) years from the time the payment was made, unless before the expiration date of that period a claim therefor is filed by the taxpayer. The three (3) year periods allowed by this section for making refunds or credit claims shall not apply in cases where the tax commission asserts a deficiency of tax imposed by this chapter and taxpayers desiring to appeal or otherwise seek a refund of amounts paid in obedience to those deficiencies must do so within the time limits elsewhere prescribed by law.