A new investigation revealed 86 per cent of sampled products carried the potentially deadly pathogen, while Salmonella was detected on 20 per cent, as well as various parasites.
Scientists say dogs and cats fed on raw meat-based diets (RMBD) can pass on the bugs by licking their human companions or simply by brushing up against them.
In recent years increasing numbers of dog and cat owners have turned to raw meat-based diets (RMBD), influenced by books such as The Paleopet Handbook, in the belief they are healthier.
But researchers believe there is no evidence for any benefit compared to mainstream dry or canned pet foods and that RMBD may even be less nutritious.
Published in the journal Vet Record, a British Medical Journal Publication, the study examined 35 RMBD products from eight separate brands.
As well as E Coli and Salmanella, scientists at Utrecht University found Listeria in 15 of the samples, a bacteria which can cause serious complications in pregnant women or in people with weak immune systems.
The team also found evidence the raw meat was carrying antibiotic-resistant bacteria, threatening to build up immunity to drugs in animals and their owners.
They wrote: “The presence of antibiotic-resistant bacteria in RMBDs could therefore pose a serious risk to both animal health and public health - not only because infections with these bacteria are difficult to treat, but also because of the potential of it contributing to a more widespread occurence of such bacteria.”
Last year a charitable scheme which sends dogs into schools to help children read, Burns By Your Side, announced it had banned the use of animals fed on raw meats because of the health risk to children.
RMBDs include raw dried dog and cat treats such as pig ears, home-prepared meats based from food sold for human consumption and commercial raw meats marketed for pets.
The Utrecht study said claims RMBDs yield health benefits had no scientific evidence supporting them, adding: “in nutritional terms, these diets are often deficient in several nutrients and may therefore lead to serious health problems, especially in young animals that are growing.”
It said the pathogens can be transferred “through direct contact with the food; through contact with a contaminated pet, such as sharing the same bed and allowing licking of the face and hands; through contact with household surfaces; or by ingesting cross-contaminated human food”.
The team said the bugs risked the health of the animals themselves, as well as their owners.
They cited evidence of contaminated RMBDs causing gastroenteritis in greyhounds and diarrhoea in young puppies.
“It is important to encourage awareness of the possible risks associated with feeding RMBDs to companion animals, and pet owners should be educated about personal hygiene and proper handling of RMBDs,” the study said.
“In addition, warnings and handling instructions should be included on product labels and packages.”
The Kennel Club said it believed adherence to RMBD was increasing.
Caroline Kisko, the organisation's secretary, said: "We would recommend that dog owners speak to their vet about which option might be best for their individual dog, particularly if they have concerns over a product.”
Michael Bellingham, Chief Executive of the Pet Food Manufacturers' Association, said: “We have seen a growing interest in raw pet food and we know from our contact with the veterinary profession that vets are getting more questions from pet owners on these diets and how they can feed them safely."
He said new PFMA guidelines set out how to handle raw meat hygienically.