Call the accountant of the supplier and specify the VAT information. If it's just a mistake of the accountant calculate the amount of VAT on their own and select it when drawing up the payment order in the line "Purpose of payment". Ask the provider correctly completed invoice for the prepayment amount, as the expense is not a primary accounting document necessary for obtaining the deduction of VAT.
If the vendor works, excluding VAT, in the line "Purpose of payment" make the payment order on this account make a mark "without VAT". Keep in mind that organizations are not VAT registered, does not issue invoices to the buyers under the provisions of article 168 of the Tax code of the Russian Federation, and to receive a tax deduction, working with such counterparty will not succeed. However, some "simplified" produce implementation documents for VAT without being a payer. If the tax Inspectorate will conduct a counter-check and establish this fact, the amount of the deduction on these instruments will have to return to the budget.
To avoid this, include in the bilateral agreements concluded with all suppliers contracts an additional condition. Specify that the provider must refund the amount of value added tax, which the organization has paid the price of the goods, works or services, if at the time of shipment and invoicing-invoices it was not VAT payer.
Call this payment a penalty, not to touch the tax. Set a fixed fine equal to the amount of VAT under this contract.
Also specify in the contract that if the supplier is not a VAT payer, he must notify and secure the obligation not to impose in this case, VAT is included in the price of goods. Therefore, the penalty will be provided in accordance with article 330 of the Civil code for failure to comply with this clause.
State in the contract price of goods without VAT. Add a clause stating that if the supplier is a VAT payer, the cost of the product increases by this amount. So, if the tax authorities establish the fact of the deduction of VAT and forced to return the money to the budget, they can be sought on the basis of the contract clauses provider, hiding the status of a "simplistic".