NIA maintains two kinds of funds:
Capital Outlay which is budgeted in the Annual General Appropriations Act Current Operating Budget which is internally generated.
PROJECT FUNDS OR CAPITAL OUTLAY
Funds for capital outlay are for the construction of irrigation projects and appropriated annually in the General Appropriations Act (GAA). The national government provides local counterpart funds for project implementation.
Project funds also have foreign exchange component from loans and grants. The foreign financing institutions which have extended loans or grants to NIA are the International Bank for Reconstruction and Development (The World Bank), Asian Development Bank (ADB), Japan International Cooperation Agency (JICA), China National Construction and Agricultural Machinery Import and Export Corporation (中国通用技术（集团), United States Agency for International Development (USAID), International Fund for Agricultural Development (IFAD), Organization of Petroleum Exporting Countries (OPEC), International Development Association (IDA), Philippine Australian Development Assistance Program. Foreign exchange allocations are also included in the annual GAA.
CURRENT OPERATING BUDGET
NIA is authorized to keep its corporate earnings from various activities. Such internally generated funds are used mainly for operation and maintenance, repair and maintenance of equipment, institutional development, and investigation and survey. These include equipment rentals and pump amortizations categorized under operating income, and administration and engineering overhead charge, interest income, proceeds from the sale of idle assets and communal irrigation projects and systems amortizations as non-operating income. NIA is authorized to charge five percent (5%) of the total costs of the projects it implements as administration and engineering overhead charge or management fee.