"When slaughterhouses cut corners on hygiene, consumers are put at greater risk," said Torbjörn Axelsson, regional manager for the National Food Administration (Livsmedelsverket).
At six out of 18 abattoirs inspected by the administration, animal carcasses had "a far too high presence of stomach and bowel contents."
"That figure is far too high. I am surprised that there are so many," Axelsson said.
Warnings have been issued to the six slaughterhouses where standards were deemed to be too low. If standards have not improved by the time of the next inspection they could lose their operating licences.
People suffering from E.coli poisoning typically experience severe bowel inflammation and bleeding. The illness often starts with abdominal cramp and diarrhea. Around 200 cases are reported in Sweden every year, according to the Swedish Institute for Infectious Disease Control.
Cattle and other animals can carry E.coli in their bowels without suffering ill effects.