However, the Efsa authors also concluded that when used indoors, for example in greenhouses, neonicotinoids do not threaten bees in the same way.
"The availability of such a substantial amount of data as well as the guidance has enabled us to produce very detailed conclusions", saidJose Tarazona, head of the EFSA Pesticide unit.
Graeme Taylor, of the European Crop Protection Association, said: "We do not dispute the possibility of risk to bees, but do not share Efsa's view on the nature of that risk".
Three such pesticides - clothianidin, imidaclroprid and thiamethoxam - had already been hit with a moratorium on use in flowering crops in 2013 following an EFSA risks assessment that linking them to bee declines.
The report said "most uses" of the three neonicotinoid pesticides, which are based on the chemical structure of nicotine and attack the nervous systems of insect pests, posed a risk to bees.
Unlike contact pesticides - which remain on the surface of foliage - neonicotinoids are absorbed by the plant from the seed phase and transported to leaves, flowers, roots and stems. In some situations, the pesticide may persist and accumulate in the soil. "The information on this phenomenon is somewhat limited, but EFSA concluded that, in some cases, bees might still be exposed to harmful level of neonicotinoids pesticides through this route".
A European vote on such a ban could happen as soon as March, and if a majority of countries vote for the proposal it will be imposed on all member states.
However, a spokesman for Syngenta, a neonicotinoid manufacturer, said: "Efsa sadly continues to rely on a [bee risk guidance] document that is overly conservative, extremely impractical and would lead to a ban of most if not all insecticides, including organic products".
"EFSA's findings place it outside the current mainstream science on bee health, as represented by recent similar assessments" by U.S. and Canadian agencies, the company said. The assessment found that bees getting in touch with nonflowering crops as well as water sources and soil were also at risk - while previous assessments had focused mainly on flowering crops, more attractive to bees.
"EFSA's conclusions can therefore not be used as a measuring stick to justify further neonicotinoid restrictions". Neonicotinoids, which are nerve agents, have been shown to cause a wide range of harm to bees, such as damaging memory and reducing queen numbers.
"While challenges to bee health remain due to a number of factors, the fact remains that the total number of beehives in the European Union is continuing to rise".