The European Commission says it is Europe's most comprehensive study so far of bee colony deaths.
Winter mortality was especially high for bees in Belgium (33.6%) and the UK (29%) in 2012-13. But in spring-summer 2013 France was highest with 13.6%.
Bumblebees and other wild bees were not studied, nor were pesticide impacts.
The study, called Epilobee, described 10% as an acceptable threshold for bee colony mortality - and Greece, Italy and Spain were among the countries with rates below that threshold.
The mortality percentages are national estimates based on representative samples. All 17 countries applied the same data collection standards, the report says.
The survey covered almost 32,000 bee colonies.
But there is also much concern about death rates among wild bees, which are vital pollinators too.
Last year the EU introduced a ban on four chemicals called neonicotinoids which are used in pesticides.
They are believed to be linked to the collapse of bee colonies across Europe, though there is a heated scientific debate over the chemicals' impact and many experts say further studies are needed.
The Commission wanted pesticide impacts to be included in the Epilobee study, but it was overruled by member states' governments.

The northbound carriageway was closed at 02:00 on Thursday at junctions five, Castle Bromwich and six, Spaghetti Junction and was not reopened until about 01:30 GMT on Friday.
A 26-year-old man driving a Saab died at the scene.
A 200m-length section across four lanes had to be resurfaced after a fuel spillage, Highways England said.
Read more on this story and other news from Birmingham and the Black Country
A Highways England spokesman said earlier: "You've got about a 200m stretch - so that's 800m across all four lanes.
"Fuel has leaked on to the carriageway and it's really got into the carriageway, so that's the problem and it's just not safe to reopen."
Traffic jams trailed back to junction four for the M42.
Drivers were stuck for hours in congestion on the M42 north from junctions six to nine and on the A446 around Coleshill.
Many of the main routes into Birmingham slowed to a crawl as people tried to find alternative routes.
BBC Travel has the latest
Two southbound lanes between junctions six and five, that were closed at about 03:00, reopened about six hours later.
Two lanes closed on the northbound carriageway of the M6 at junction 3A near Coleshill after a separate traffic collision at 12:30 reopened by 13:00, said Highways England.
Drivers expressed their anger on social media at being caught in the congestion in and around Birmingham during Thursday's rush hour.
Paul Davis tweeted at 10:00 he had only managed to drive six miles after leaving from Sutton Coldfield at 07:00.
Earlier Virgin Trains said it had advised its ticket managers at Birmingham International to use discretion towards commuters in light of the disruption.
Police had hoped to reopen the northbound lanes at about 07:30 on Thursday, but Highways England said extensive damage had been caused and assessment and repair work was being carried out.
Diversions were put in place but motorists were caught up in long delays on surrounding routes, particularly on the A38.
West Midlands Ambulance Service said the lorry driver in the collision was shaken but uninjured.

Kluber struck out eight of the first nine outs registered and Roberto Perez hit two home runs as the Cubs endured a miserable return to the season finale.
The Cubs' last World Series win was in 1908, while the Indians clinched their most recent title in 1948.
Game Two of the best-of-seven series begins at 00:08 BST on Wednesday.
The first pitch has been brought forward an hour because of the threat of rain in the Cleveland area.
A new study covering 17 EU countries says that far more honeybees are dying in the UK and other parts of northern Europe than in Mediterranean countries.
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Part of the M6 in Birmingham was closed for almost 24 hours after a fatal collision involving a lorry and a car.
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A superb pitching display from Corey Kluber helped the Cleveland Indians to an emphatic 6-0 win over the Chicago Cubs in the World Series opening game.