GST is calculated differently on Customs payments. The GST portion of the item purchased is charged separately to the item itself, and is charged along with the other Customs duties and fees. This is for high value items (over $1000) that will be used for business purposes.
See here how to handle this in Farm Focus:
1) Click on the + Record Invoice and select GST All option:
The Payment Request form shows the charges and fees as well as the GST portion for the item purchased as follows:
2) The GST amount is $9,106.50. Select the correct code and enter in the GST amount to be paid or received and click Apply.
3) The invoice will auto-calculate with a contra against the same code to ensure the GST amount payable or receivable is correct. Click Save to save this invoice, or match to a transaction.
For more information on Customs charges or to calculate your GST and duties, use the "What's my duty" Calculator or visit Customs.govt.nz