DEFRA is being forced to repay more than £160m to the European Commission for breaking rules over administering farm subsidies.
EU states have been ordered to hand back £225.4m (E265m) of farm money misspent between 2004 and 2007.
Of all the countries, England was the worst offender, with more than 70% of the bill (£160.9m) handed to DEFRA for problems between 2004 and 2006.
Mapping problems left the department with a £116.5m fine, while it was billed £44.6m for problems the Rural Payments Agency had with setting up the single payment system.
Agricultural commissioner Dacian Diolos said the decision to hand down the fines was to “achieve the best possible control of farm spending”.
“[We need to] verify that taxpayers’ money is not being misspent,” he added.
A DEFRA spokeswoman said the department had already known about the fines and accounted for them in its budgets.
“The fine is not going to impact on the delivery of services to farmers,” she added.