The AAT has held that an assessment issued to the taxpayer ("the Company") for GST on GST free supplies was excessive.
The Company paid GST on supplies to an overseas entity on a quarterly basis. It sought and obtained a ruling that the supplies are GST-free. Encouraged by this, after more than four years (and out of time), the Company lodged a revised GST return for the June 2008 quarter and the Commissioner promptly refunded an amount equivalent to the excess GST the Company had paid, namely, $32,098. Soon thereafter, however, the Commissioner issued an assessment counteracting the Company’s revised GST return, applying the refund amount as GST for which the Company was liable. Specifically, the $32,098 refund was included as an integer in the calculation of the ‘net amount’ for the period, being recorded as "GST on sales".
The AAT said at para 88:
"Even if the Company’s action lodging a revised BAS for the June 2008 quarter was out of time, the action gives rise to a deemed assessment that cannot be overcome by the Commissioner issuing an amending assessment to reinstate the net amount originally calculated by the Company on the basis of assumptions in the past that are not correct [ie that GST was payable in respect of GST-free supplies]. An assessment of this kind is not within the terms of s 35-5 of the GST Act."
The Company's objection against the assessment was upheld.
Swanbat Pty Ltd and FCT  AATA 891 (AAT, Webb M, 13 December 2013).