In Sweden, 46 incidences of rape are reported per 100,000 residents, according to the EU study.
This figure is twice as high as in the UK, where 23 cases are reported per 100,000 residents, and four times that of the other Nordic countries, Germany and France. The figure is up to 20 times the figure for certain countries in southern and eastern Europe.
"There is not one single explanation for the high figures," lead professor Liz Kelly told the TT news agency.
"People are better at reporting [rape] here than elsewhere, the definition of what constitutes rape has become broader, and there is a greater willingness among Swedish women to report rape in relationships."
"In order to ascertain whether the real incidence is higher, more research is required," said Professor Kelly.
The study, which is financed by the Brussels-based EU fund Daphne II, compared how the respective judicial systems managed rape cases across eleven EU countries.
More than 5,000 rapes are reported in Sweden per annum while reports in other countries of a comparable size amounted to only a few hundred.
The figures are however distorted by the fact that in many countries only assault rapes by strangers and aggravated rapes by people known to the victims are reported - as was the case in Sweden 40 years ago.
Many of the reported rapes were linked to nightlife and partying, specifically after-club parties in private homes. Most victims were young, and half had consumed alcohol.
The Daphne II fund ran from 2004-2008 and was set up by the European Parliament as a specific programme to prevent and combat violence against children, young people and women and to protect victims and groups at risk.
In 2007 Daphne III was launched to continue the work and is funded up to 2013.
Correction: An earlier version of this article incorrectly stated that "rape simply appears to be a more common occurrence in Sweden than in the other EU countries studied, the researchers argue." This was a direct translation from Swedish news agency TT, which later amended its original article to include clarifications from Professor Liz Kelly.
The headline has been updated to reflect these clarifications.