Five-year-old Mason Jones, a pupil at Deri primary school, near Bargoed, Caerphilly, was killed by the bug which affected more than 40 schools and 158 people in an outbreak in south Wales last year.
Dr David Salter, Wales's acting chief medical officer, looked at the systems in place before and during the outbreak to ensure lessons could be learned. His report makes 22 recommendations on reviewing food legislation and improving hygiene in school.
Local authorities have been issued with seven recommendations, including the need to work with the Food Standards Agency to introduce any new measures to improve food hygiene.
Councils have also been told to look into arrangements for school cleaning and to ensure that toilets have soap and hot water.
Peter Clarke, Wales's children's commissioner and a long-standing campaigner for better school toilets, said: "I am pleased to see that food hygiene and clean toilets are part of the recommendations.
"We don't know whether that played a part, but I have been told that it is likely. We now need to ensure that all children in Wales have access to the basic facilities of hot water and good toilets."
Mr Clarke said a good start had been made but there was still a long way to go before the outcome of the police investigation and public inquiry.
Dr Salter's report also makes eight recommendations for the FSA. It calls on it to review existing food legislation and guidance to councils on how often premises should be inspected and whether further legislation is needed.
It is also being asked to look into whether the law was applied correctly when dealing with John Tudor and Son, the meat supplier linked to the outbreak. Dr Salter's review was limited because of an on-going investigation by South Wales Police. A public inquiry, to be chaired by Professor Hugh Pennington, is also dependent on the outcome of the police work.
Among three recommendations for the Assembly government was a need to resolve the difficulties of trying to run a review alongside a police investigation.
There are three recommendations for the National Public Health Service and the Outbreak Control Team, which include the need for better communication with the public. Dr Salter's report also recommends that the Wales Centre for Health should work with the Outbreak Control Team to improve communication with the public during an outbreak.
He said: "The E. coli outbreak was the largest in Wales and it was essential that we looked at what happened."
Dr Brian Gibbons, Assembly health minister, said all organisations should try to implement the recommendations quickly.