One of the methods to work around this would require the possibility to be able to post the VAT tax paid to the revenue authority by the customs broker (on his client's  behalf) which is then re-billed to his client among several other direct COGS items on their invoice, on the VAT side with ZERO line item value.

A Typical Customs Broker Invoice Example where Goods have been prepaid directly to the supplier (Foreign currency prepayment) would look like this:

CUSTOMS BROKER LTD - INVOICE
Clearing of 1 Pallet Various imported Goods from Supplier XYZ.
1 Customs Duties                                12,345.00      VAT- Nil -      0.00
2 Storage                                                  100.00     VAT 15%    15.00
3 VAT PAID to customs                           2,000.00     VAT- NIl        0.00
4 Local Transport                                      650.00     VAT 15%     97.50
5 Customs broker fees                           1,200.00     VAT 15%   180.00

Total Payable                                        16,295.00    Total VAT     92.50
Line 3 is a problem.
When processing this invoice it would be necessary to input the VAT Paid to Customs amount LINE 3 (2,000.00) DIRECTLY in the invoice TAX column with no amount (but a description of reason of this tax) in the line item, so that it is accounted properly as input VAT and picked up by the VAT TAX report.

What is the best way to handle this in FA ?

Thanks / Regards