The children, the youngest of whom is 20 months old, had eaten defrosted hamburgers made by the French company SEB which said the meat was possibly taken from animals slaughtered in Germany and processed in France.
"There's meat from Germany, there's meat from Belgium and from Holland," SEB chief executive Guy Lamorlette told news agency AFP. "There are several suppliers. We will have to await the test results to say which is contaminated."
The "Steak Country" burgers were bought in French branches of German supermarket Lidl. SEB said it had recalled them and Lidl said it had removed them from its shelves in France.
Health authorities said the infection was a rare strain of the E. coli bacteria and was not connected to the recent outbreak in Germany, though SEB said the meat was sourced there.
"They are in a serious but not worrying state. Their lives are not at all in danger," said a spokesman for the Regional Health Agency (ARS) in Lille, northern France, where the children were hospitalized on Wednesday.
The ARS official said the children had suffered from bloody diarrhoea, which also struck victims of the outbreak in Germany which has been blamed on infected vegetable sprouts.
The French infections "have no link at present with the recent epidemic in Germany," the official added.
Despite a general reduction in the rate of new infections with the EHEC bacteria in Germany, the 38th person died on Thursday according to public health authorities.