The admission is hugely embarrassing for Germany, which had previously blamed Spanish cucumbers for the bug.
Beansprouts are a common ingredient in salads and stir frys, but have previously been blamed for major health scares. They were held responsible for a serious outbreak of Salmonella in Britain last year and 17 E.coli-related deaths in Japan in 1996.
On Sunday evening, Gert Lindemann, agriculture minister in the northern state of Lower-Saxony, said a company that grew bean sprouts had been shut down and further test results were expected on Monday.
"There was a very clear trail (to this company) as the source of the infection," Mr Lindemann said in a news conference. He urged consumers in northern Germany to refrain from eating all types of sprouts.
"It is the most convincing...source for the E.coli illnesses," he said.
