The financial statements of the NCUA’s four main funds are presented fairly but there are serious difficulties in the agency’s financial accounting, according to an independent audit released Monday.

The audit by KPMG found that the reports of the NCUA Operating Fund, the Central Liquidity Facility, the Community Development Revolving Loan Fund and NCUSIF “present fairly, in all material respects,’’ their financial positions.

But the report found a “significant deficiency’’ in the agency’s financial accounting for its Operating Fund, including problems  by management  to provide key documentation related to property and equipment, a “lack of efficiency,’  in record keeping and financial close procedures, and a lack of documentation of activities aimed at confirming journal entries documenting that certain transactions were made as approved.

The agency responded that it had already made some improvements to its accounting system and would make more of them to respond to the deficiencies.