Roger Houldey, a part-time beekeeper from Gloucestershire, was forced to move his hives after he discovered a field of GM oilseed rape had been planted three miles away.
The Bee Farmers Association is advising its members their hives should be at least six miles from any trial sites.
Experiments carried out on nine pots of honey brought from shops near GM sites revealed traces of genetically-modified pollen in two of them.
The tests were commissioned by the environment group Friends of the Earth which is now calling for an immediate ban on all outdoor testing of genetically-modified oilseed rape and maize.
Roger Houldey, a part-time beekeeper from Gloucestershire, was forced to move his hives after he discovered a field of GM oilseed rape had been planted three miles away.
"A GM trial site has been given the go-ahead very close to my hives, yet I wasn't even consulted," he said.
Mr Houldey said Britain's big honey buyers will not consider his product unless he can guarantee it is GM free.
"They won't take our honey unless we give them a written undertaking," he told BBC News.
Livelihoods threatened
The tests on the honey were carried out by Dr Andreas Heissenberger, an independent scientist at the Federal Environment Agency in Austria.
"It proves it is getting into the food chain and it must come from the trials," he said.
Friends of the Earth said the discovery confirms fears that GM crops threaten the livelihoods of neighbouring farmers and bee keepers.
But GM farmers are under no obligation to consult their neighbours about the trials, Friends of the Earth said.
The Bee Farmers Association - which represents 350 commercial bee farmers throughout the country - wants compensation for the loss of income incurred when members are forced to move their hives.
Pete Riley, senior food campaigner at Friends of the Earth said: "We now have evidence that GM crops can contaminate honey.
"It is essential that the government takes immediate action to protect this multi-million pound industry from the GM threat.
But the GM industry said there was no scientific or legal reason to move the hives so far away and they announced they are planning to study the new research.