More than a third of all honeybee colonies in England died over the winter, according to figures from the British Beekeepers Association, the worst losses since its winter survival survey began.

On average, 33.8 colonies in every 100 perished over the long winter of 2012-13 compared with 16.2% the previous winter. In the south-west of England, more than half of all colonies were wiped out and in the northern part of the country 46.4% didn't survive.

In Scotland and Wales, honeybees fared no better. The Scottish beekeepers association, which has yet to complete its annual survey, predicts losses of up to 50%. And bee farmers in Wales have reported 38% losses.

The BBKA attributed the alarming high bee mortality to the poor weather during 2012 continuing into 2013 and exacerbated by the late arrival of spring.

"The wet summer prevented honey bees from foraging for food, resulting in poorly developed colonies going into winter. When they could get out there was a scarcity of pollen and nectar. Honeybee colonies which are in a poor nutritional state become more vulnerable to disease and other stress factors," said a BBKA spokeswoman.

Many beekeepers also reported incidence of "isolation starvation", when the cluster of bees in the hive becomes too cold to move close enough to eat their food stores in another part of the hive, and so starve.

But there are fears that the death toll for bees in England could be even higher, since the BBKA survey of 846 members closed at the end of March before the arrival of spring.

"April this year was very cold, and the start of May, so bees were confined to the hive for much longer and we still had bees dying from starvation in May. So losses could be much more serious," said Glyn Davies, a beekeeper from Devon and former president of the BBKA.

He said the south-west was particularly badly hit because of the relentless rain. "It was the wet, wet, wet, wet summer followed by an enormously long winter. I've never seen anything like it in the 35 years I've been keeping bees," said the 74-year-old beekeeper.

The winter bee losses come just weeks after EU member states voted for a suspension of three pesticides alleged to cause serious harm to bees.

Francis Ratnieks, professor of apiculture at University of Sussex, said pesticides weren't the cause of the high bee mortality: "It was the worst summer ever. I had my own bees starving to death in the summer. It is nothing to do with pesticides; bad weather is enough of an explanation. It's not healthy for bees to be trapped in their hives during the summer. Some queen bees couldn't get out to mate and confined bees are more likely to get nosema [a gut parasite] and viruses from the varroa mite."

When the BBKA survey began in 2007-08, winter bee mortality was 30.5%. Since then losses had been steadily falling.

The government's National Bee Unit says its initial 2012-13 findings of around 30% winter bee losses are the highest recorded loss since its bee inspectors began to formally gather their own figures five years ago.

Mike Brown, head of the NBU, commented, "These figures are not surprising given the harsh winter and long cold spring which followed on from an extremely poor summer last year. The National Bee Unit has continued to offer colony husbandry advice to beekeepers through these prolonged periods of inclement weather."

The Scottish government has announced £200,000 in funding to help bee farmers restock their colonies, but a Department for Environment, Food and Rural Affairs spokeswoman said: "We do not provide government money for restocking bees. We are working with beekeepers to provide support and training to help them ensure the health of their bees."