The study of 32,000 bee colonies across 17 EU member states from late 2012 until summer 2013 found winter mortality rates ranged from 3.5% to 33.6%.
The winter of 2012-13 was particularly cold and the highest mortality rates were in northern countries with harsher climates.
During the beekeeping season, when the insects are active, mortality rates were between 0.3% and 13.6%.
“It’s the first major study of pests and diseases that affect honey bees. A lot of it seems very encouraging,” said Tom Breeze, a specialist in bees at the University of Reading but who was not involved in the study, which was made public by the European Commission this week.
By comparison, US beekeepers lost nearly a third of their colonies last winter as part of a largely unexplained decline in the population that could affect food supplies.
The study found that overall prevalence of the bee diseases American foulbrood was low in all the monitored EU member states, ranging from zero to 11.6%.
European foulbrood was even lower. Only five member states observed positive cases and the clinical prevalence exceeded 2% in only one member state.
Varroosis, a disease caused by a mite, was, however, observed in nearly all the monitored member states.
The survey was financed by 17 of the 28 EU member states which took part and by the commission, which contributed €3.3m. It said the study would be followed up with further research.
Greenpeace welcomed the study as far as it went, while saying that it left out analysis of the impact of pesticides and changes to biodiversity.
“This is the first year in which some sort of monitoring has started. Finally it’s a first step in the right direction,” Greenpeace’s EU agriculture policy director Marco Contiero said.
Last week, the Red List of the International Union for Conservation of Nature found that almost a quarter of Europe’s bumblebee population is at risk of extinction because of loss of habitats and climate change.
The commission said current indicators showed that wild bees, closely related to the honey bees and also vital pollinators, were in “a worrying decline”.
It has banned the use of certain pesticides, known as neonicotinoids, suspected of harming bees. They are produced mainly by Germany’s Bayer and Switzerland’s Syngenta.
In addition, EU policymakers are trying to address bee health by insisting on measures such as crop diversification as part of reforms to the Common Agricultural Policy.