A team at Dundee University studied more than 600 colonies across the country in 2011/12.
Of 274 colonies checked in the east of the country, 58, or 21%, failed, but just 14 of 286 colonies failed in the west, about 5%.
Scientists believe the presence of intensive agriculture and large areas of oilseed rape in the east could be linked to the difference.
But they criticised the fact that data on pesticide use is not gathered, saying the current system makes it impossible to properly determine what is causing honey bees to die.
The study was carried out with the help of the Scottish Beekeepers Association.
Dr Christopher Connolly of the university's division of neuroscience, who led the research, said he was stunned by the findings.
He said: "It's a fantastic lead. If only we knew what was being used in those places. What we do have in the east and not the west is intensive agriculture.
"It could be that the lack of natural habitat is the cause. It may be that bees and other pollinators may not be getting such a balanced diet. In the west, it's largely wild crops that they are feeding on. It could be that the intensive agriculture and intensive levels of pesticides are contributing to the failure."
There were also marked differences in death rates in the east. Colony losses in parts of Fife were as high as 30% while Edinburgh lost less than 6%.
A further study led by Dr Connolly analysed colony failure rates over winter. Of 89 colonies which had fed on oilseed rape, 27 failed. Just 13 out of 82 colonies which had not fed on rape died.
Dr Connolly believes nicotine-based pesticides, neonicotinoids, may contribute to deaths of bees feeding on the crop.