You need to enter the VAT via a Purchase Invoice as though the govt authority had sent you one but you also need to add an extra line to that Purchase Invoice.
Let say the value of the VAT is 100 being 10%, so the imported item was worth 1000.
On the first Purchase Invoice Account line you would enter the item as per a normal purchase.
On the second Account line re-enter the item but with a matching negative number and NO tax.
You can pick any account but use the same one for both lines.
If you go to this topic Journal entry for vat invoice you will see an example.