Ireland's member on the European Court of Auditors said the court has not given a "full statement of assurance" on EU spending for the financial year 2011..
Speaking after the publication of the court's annual report, Kevin Cardiff said that in terms of "the legality and regularity of transactions" of EU spending, the court would not, in effect, be signing off on 2011's accounts.
He said: "At a time of financial crisis the proper spending of all public moneys is all the more important."
The report of the Court of Auditors found an error rate of 3.9% for the EU budget as a whole, compared to 3.7% in 2010.
Mr Cardiff, who took up his position in Luxembourg last February, said the majority of spending errors were the fault of member states, which are required to monitor and control the spending of EU funds.
The report found that the biggest problems were in outlays on rural development, fisheries and health with the majority of errors arising from "misapplication or misunderstanding" of EU rules.
A handful of cases of suspected fraud were reported to the EU's anti-fraud office.
The report found that in 2011 the EU spent €129.4bn.
Of this, 80% was spent on agriculture and cohesion policies, where the task of implementing the budget is shared between the European Commission and member states.
"The systems in member states are not catching errors," Mr Cardiff said.
The European Commission is responsible for checking 5% of the total number of outlays, although its role is to check systems "after the event".
Mr Cardiff said that by and large the number of errors recorded in Ireland was small.
Court of Auditors president Vitor Caldeira said: "This annual report's message is consistent with previous years', but this year it matters more than ever.
"With Europe's finances under severe pressure, there remains scope to spend EU money more efficiently and in a better targeted manner.
"Member states must agree on better rules for how EU money is spent, and member states and the Commission must enforce them properly."
The report is likely to be seized on by British euro-sceptics in the run up to next week's summit of EU leaders on the size of the next seven-year EU budget.
The EC has proposed a seven-year budget of over €1 trillion, but there will be strong pressure from a number of countries for that figure to be reduced - possibly by up to €200bn - during next week's two day negotiation.
British Prime Minister David Cameron has said that he will veto any deal if it does not represent at the very least a freeze in the size of the budget compared to the previous budget round (2006-2013).