The certifying authority of the programme is the National Fund Directorate at the Ministry of Finance of Republic of Bulgaria. The Certifying Authority receives the payments made by the Commission and transfers funds to the Managing Authority at the Ministry of Regional Development and Public Woks and is responsible for:

• drawing up and submitting to the Commission certified statements of expenditure and applications for payment;
• certifying that: the statement of expenditure is accurate, results from reliable accounting systems and is based on verifiable supporting documents; the expenditure declared complies with applicable Community and national rules and has been incurred in respect of operations selected for funding in accordance with the criteria applicable to the programme and  complying with Community and national rules
• ensuring for the purposes of certification that it has received adequate information from the managing authority on the procedures and verifications carried out in relation to expenditure included in statements of expenditure;
• taking account for certification purposes of the results of all audits carried out by or under the responsibility of the Audit Authority;
• maintaining accounting records in computerised form of expenditure declared to the Commission. The managing authorities and the audit authorities shall have access to this information. At the written request of the Commission, the certifying authority shall provide the Commission with this information, within ten working days of receipt of the request or any other agreed period for the purpose of carrying out documentary and on the spot checks;
• keeping an account of amounts recoverable and of amounts withdrawn following cancellation of all or part of the contribution for an operation. Amounts recovered shall be repaid to the general budget of the European Union prior to the closure of the crossborder programme by deducting them from the next statement of expenditure;
• sending the Commission, by 28 February each year, a statement, identifying the following for each priority axis of the cross-border programme: the amounts withdrawn from statements of expenditure submitted during the preceding year following cancellation of all or part of the public contribution for an operation; the amounts recovered which have been deducted from these statements of expenditure; a statement of amounts to be recovered as at 31 December of the preceding year classified by the year in which recovery orders were issued.