IPA funding in Turkey is mostly implemented under indirect management, by those entrusted Turkish institutions which meet all the necessary requirements in line with the EU's Financial Regulation. Some activities also come under direct management; in other words, the implementation of the budget is carried out directly by the European Commission's services.

In the indirect management system, the Ministry of EU Affairs as the National IPA Coordinator (NIPAC) holds key responsibilities for overall coordination of the system, including the programming and monitoring processes.

The Undersecretariat of the Treasury functions as National Authorising Officer (NAO), holding the overall responsibility for the financial management of IPA funds in Turkey, and ensuring the legality and regularity of expenditure of EU funds. The NAO is responsible for the management of IPA accounts and financial operations as well as the effective functioning of the internal control systems.

The Central Finance and Contracts Unit (CFCU), which is administratively linked to the Treasury, has the responsibility for the budgeting, tendering, contracting, payments, accounting, and financial reporting aspects of IPA procurements.

There are also four additional contracting authorities entrusted with implementing the IPA funds that deal with multi-annual sector operational programmes:

• Ministry of Environment and Urbanisation for the environment and climate action sector; 
• Ministry of Science, Industry and Technology for the competitiveness and innovation sector;
• Ministry of Transport, Maritime Affairs and Communication for the transport sector; and
• Ministry of Labour and Social Security for the sector education, employment and social policies.

Lastly, for the IPA Regional Development programme (IPARD), the Agriculture and Rural Development Support Institution is the agency responsible for the implementation and payments of IPA funds in selected provinces.