DEFRA has been ordered to repay more than £24m to the European Commission for failing to follow EU rules.
The UK was one of 10 member states told to return a total of almost €530m (£469m) to the EU budget because of poor controls and non-compliance with rules on agricultural expenditure.
The UK faces repayments of €26.95m (£23.7m) for weaknesses in “the recognition of producer organisations” and deficiencies in verifying the value of its fruit and vegetable production.
It has to pay back a further £252,103 for undue charges for rendering and transporting intervention stocks and for claims for EU financing for dead animals.
DEFRA will have to repay an additional £7,342 for errors relating to export refunds.
The repayments relate to errors made by member states between 2006 and 2009, but the UK was not the worst-offending country of the group.
Greece was ordered to pay back more than €259m (£230m) for errors relating to its olive industry and land parcel identification schemes.
Meanwhile, Spain had to repay more than €108m (£95m) for issues surrounding environmental management and checks on its olive oil industry.
The commission carries out more than 100 audits every year to check countries are properly managing CAP payments and checking farmers’ claims for direct payments.
It has the power to claw back funds if it decides member states are not spending EU funds properly.
A DEFRA spokeswoman said: “The Producer Organisation Working Party, consisting of DEFRA, the RPA and representatives of Producer Organisations, has looked at guidance for the scheme and has now clarified rules for the sector to ensure they meet the EU requirements for the fruit and vegetables regime.”