With the VAT threshold being R1 million, your tenderer is obliged to register for VAT the moment he/she/it gets the tender, surely.
I'd suggest you either have to add the 14% that the tenderer has neglected to account for in the tender to compare apples with apples and/or consider the tender submission as incomplete and proceed accordingly.
I'd also suggest that the tenderer's capacity to deliver should be looked at quite closely - but I'm sure you do that anyway?
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