The biggest concentrations of suspected false claims were in three countries: Romania, Bulgaria and Hungary.
These are among the main conclusions of the annual report of the EU anti-fraud office, Olaf.
The Brussels-based fraud-busting agency said that an estimated €888m was disbursed to dishonest claimants last year, a slight decline from €901m the previous year.
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The report, published on Tuesday, said that fraudulent claims of EU funds in 2015 was equal to 0.6 per cent of the EU budget.
Olaf, which has come under fire over the effectiveness of its work in the past, investigated nearly 1400 allegations of fraud in the past year.
These include €1.3m given to modernise a vegetable chilling plant in Bulgaria.
Olaf said they found the equipment supplier and the factory owner were the same person who, it said, had inflated the price.
In another cited case, €2m of EU aid was sent to an ecology project in Africa whose operators, say OLAF, were charging different international donors for the same work by supplying "systematically false information".
The annual report suggests that national prosecutors themselves could do more to crack down on EU fraud. Out of 317 cases sent to national prosecutors, 148 resulted in indictments, a rate of 47 per cent.
At a news conference, Olaf Director General Giovanni Kessler said that he did not believe there was widespread corruption in 2015. He did, however, repeat his call for the creation of a prosecutor's office for the EU which could have greater powers than Olaf to investigate fraud.
Reacting to the report, Jonathan Arnott, a member of Parliament's budget control committee, said, "With such outrageous levels of waste exposed again we must ask why are we sending money to the EU's sinkhole in Brussels?
"People's hard earned money should not be chucked away in this scandalous manner. If you break the link between who people elect and how those in power spend the taxpayers' money then wholesale fraud and waste is inevitable.
"If we cannot hold accountable and get rid of those who spend our money then financial and political corruption will continue to go hand in hand."
More comment came from S&D group leader Gianni Pittella, who said the report brought "positive news" for European citizens.
Pitella said, "It clearly shows that Olaf is a strong and independent organisation with an impressive record in the last few years. Since 2012, it has increased the number of concluded investigations by 93 per cent and opened 86 per cent more investigations. These figures show that Olaf's impact and contribution in protecting the EU budget is indisputable.
"A strong Olaf, with an increased capacity to fight fraud, ensures that EU money reaches the people and projects where it is most needed. Olaf's work in 2015 is proof of how seriously EU institutions take the fight against fraud and corruption. It shows the EU is both willing and capable to tackle fraudulent use of the EU budget and can safeguard the money of European citizens."
His colleague, Ines Ayala Sender, S&D budgetary control coordinator, said, "In addition to its investigation and coordination cases, in 2015 Olaf organised several Joint Customs Operations. Olaf has progressed in its efforts to fight the illicit trade in tobacco products, helping national authorities seize over 619 million cigarettes in 2015.
"The Olaf report offers for the first time a comparison between the financial recommendations issued by Olaf and the financial impact of irregularities detected and reported by member states, which makes Olaf useful not only for improving the EU legal framework, such as the European Public Prosecutor Office (EPPO), but also feeds in the current European debate for a results-oriented budget and performance."
A European Commission spokesperson said it had "zero tolerance" for fraud against the EU budget, adding, "OLAF's work is part and parcel of the efforts to uncover and prevent fraud in the member states and to get money returned to the taxpayers."