The two bodies conducted a study and said that they "strongly recommend to advise consumers not to grow sprouts for their own consumption and not to eat sprouts or sprouted seeds unless they have been cooked thoroughly".
The report by the European Food Safety Authority in Italy and the European Centre for Disease Prevention and Control in Sweden said sprouts are often sold as mixes and "during re-packaging cross-contamination cannot be excluded".
The risk assessment study also said doctors "should be encouraged to report new HUS (Haemolytic Uremic Syndrome) cases in a timely manner".
Raw fenugreek sprouts have been seen as a healthy ingredient for salads.
At least 48 people have died from an outbreak of a killer strain of E.coli bacteria centred in Germany and blamed on organic vegetable sprouts.
There has also been a separate outbreak in France linked by the government to a British sprout company in which 10 people have been taken ill.