zidek wrote:company is registered for VAT in Slovakia. Slovakian tax office said to us pay VAT in Slovakia as well. I think they just don't know how to help us. Thank for help anyway.
In answer to your question - I think your best bet is to go back to your supplier. If they have got your Slovak VAT no and the commercial transport evidence they need they should revise their invoice and treat it as an intra community dispatch.
If you arranged transport of goods then you may need to provide your supplier with copies to satisfy their requirement else you may suffer double taxation as you suggest you have.
If the UK supplier refuses then you may recover the VAT via 8th directive (via Slovak online portal) - although if HMRC see this as a proper EC dispatch then it's not properly chargeable VAT and will not refund you, instead they will suggeest you go back to your supplier.
If goods went direct to your customers in Czech / Poland then you could have used triangulation. Not sure if its practical to do this retrospectively.