Section 29 of the Principal Act is repealed and the following section is substituted:

29.     Refund

(1)  The Commissioner, if satisfied that a person has overpaid an amount, is to –

(a) refund the overpaid amount; or

(b) apply the overpaid amount against any liability of the person under a taxation law, or another Act of which the Commissioner has the general administration, and refund any part of the overpayment that is not so applied.

(2)  The Commissioner may only take an action under subsection (1) in relation to an amount that a person has overpaid, if –

(a) the person has lodged an application under section 28 in relation to the overpayment; or

(b) the overpayment has been identified during an investigation conducted in accordance with Part 9 or Part 9A .

(3)  A person is not, after 3 years from the date on which the person has overpaid an amount, entitled to a refund of the amount or to have such an amount applied against any liability referred to in subsection (1)(b) , unless an application is lodged under section 28 in relation to the amount before 3 years from the date on which the person has overpaid the amount.