More than 30 separate scientific studies have found a link between the neonicotinoids, which attack insects' nerve systems, and falling bee numbers.
The proposal by European Commission - the EU's legislative body - to ban the insecticides was based on a study by the European Food Safety Authority, which found in January that the pesticides did pose a risk to bees' health.
"This decision is a significant victory for common sense and our beleaguered bee populations," said Andrew Pendleton of Friends of the Earth.
Marco Contiero, EU agriculture policy director for Greenpeace, said the vote "makes it crystal clear that there is overwhelming scientific, political and public support for a ban".
Luke Gibbs, head of corporate affairs in North Europe for Syngenta said the EC had failed again to convince all member states.
"The ban has been wrongly presented as a silver bullet for solving the bee health problem," he said. "Instead of banning these products, the commission should now take the opportunity to address the real reasons for bee health decline: disease, viruses and loss of habitat and nutrition."
Green groups and some scientists say the effects of the neonicotinoids are particularly devastating as the pesticide is applied to the seeds. That means it is present not only in the leaves which the insects eat, but also the pollen.
Farmers, however, say the insecticides are vital to prevent crops being destroyed by pests including beetles and aphids.
Reaction from the scientists reflected this divide. Professor Lin Field, head of biological chemistry and crop protection at Rothamsted Research, said he feared the decision was based on "political lobbying" and could cause governments to overlook other factors contributing to declining bee numbers, such as climate change and viruses spread by mites.
But Dr Lynn Dicks, a research associate at the University of Cambridge, said that despite the contradictory studies, the EU was right to err on the side of caution.
"This is a victory for the precautionary principle, which is supposed to underlie environmental regulation."
- Independent
How they voted
For: Belgium, Bulgaria, Cyprus, Denmark, Estonia, France, Germany, Latvia, Luxembourg, Malta, Netherlands, Poland, Slovenia, Spain, Sweden.
Against: UK, Czech Republic, Italy, Hungary, Romania, Slovakia, Austria and Portugal
Abstained: Ireland, Greece, Lithuania, Finland.
- AFP