Viruses were most prevalent in Bulgaria and Hungary, the survey of 30 countries reveals.
The 2010 figures, released by the EU's statistics office to mark Internet Safety Day, show the safest countries were Austria and Ireland.
The figures also detail financial losses online.
They show that 3% of net users in the 27 EU states lost money due to phishing attacks or fraudulent payments.
Phishing involves using fake websites to lure people into revealing details such as bank accounts or login names.Latvia recorded the highest rate of this kind of fraud with 8% of its internet users affected, followed by the United Kingdom (7%), Malta and Austria (both 5%).
The survey covered more than 200,000 computer users across the 27 countries in the European Union and was conducted during the second quarter of 2010.
The EU statistics office said the survey results were probably lower than actual infection rates as the numbers only included users who realised they had an infection. Although the EU figures focus on viruses that infect PCs, security firms have warned that other devices now face similar threats.
In its fourth-quarter threat report for 2010, security firm Mcafee said that it has seen a 46% increase in malware that targets smartphones, compared to the same period in 2009.Numbers suggest that smartphones are becoming more widespread than PCs, meaning they are becoming an increasingly lucrative target for scammers and hi-tech thieves.
Manufacturers shipped 100.9 million smartphones globally in the fourth quarter, compared to 92 million PCs, according to research firm IDC.
Much of the malware targeting smartphones was spread via PDFs and Flash software, Mcafee said.
However, the number of infections targeting mobile devices is still relatively small, with just 967 threats recorded by Mcafee in the fourth quarter of 2010.
In early January, according to some estimates, the number of viruses targeting PCs hit 50 million.