A "rapid risk assessment" conducted by the EFSA and the European Centre for Disease Prevention and Control (ECDC), "has thus far shown" that Egyptian seeds exported in 2009 and 2010 may be implicated, it said in a statement.
"There is still much uncertainty about whether this is truly the common cause of all the infections as there are currently no positive bacteriological results," it stressed.
At least 48 people have died from an outbreak of a killer strain of E. coli bacteria centred in Germany, 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 were taken ill.
Sweden on Tuesday say it had detected the first case of infection in someone who had no link to Germany.
All the deaths so far were in Germany, except for a woman in Sweden who died after being infected in Germany.
The statement said the 2009 lot appears to be linked to the outbreak in France, and the 2010 lot to that in Germany.
"This link does not explain the most recent case in Sweden, currently under investigation, and in which thus far no consumption of sprouts has been implicated."
The agencies said they had requested an urgent probe of the distribution of seeds from the two lots through Germany and Europe.
"The export of some of the seeds imported from Egypt to another company in the UK, from where the seeds were exported to France, demonstrates the necessity of this information."