The latest figures from the Food Standards Agency (FSA) shows 9.5% of samples from M&S tested positive for campylobacter at more than 1,000 "colony forming units" per gram of skin.
The ongoing survey found Sainsbury's ranked the best of the major nine retailers, with 2.6% of its chickens testing positive for the bug at the highest level.
A total of 1,492 fresh, shop-bought whole chickens were tested across supermarkets and other outlets, such as local butchers, between August and December 2016.
Lidl ranked second from the bottom of the table at 6.9%, followed by Aldi (6.7%), Co-op (6.1%), Asda (6%), Tesco (5.7%) and Waitrose (5.2%).
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Campylobacter is the leading cause of food poisoning in the UK and makes 280,000 people ill each year.
However, the FSA said the figures showed levels of campylobacter in chicken continued to decline, and there had been a 17% decline in the number of laboratory reports of human cases of campylobacter in 2016.
Overall, 7% of chickens tested positive for campylobacter within the highest band of contamination, down from 12% for the same period in 2015 and 20% in 2014.
Among the nine retailers with the highest market share, 5% of chickens tested positive for campylobacter within the highest band of contamination.
FSA chairwoman Heather Hancock said: "The challenge we set of reducing the number of people who get ill from campylobacter has been achieved.
"In the absence of any other clear indicators, we can reasonably say that the work that we and the food industry have done from farm to fork has given us this really positive result for public health.
"We commend the efforts of the larger retailers and the major processing plants who supply them, all of which have shown significant improvement and many have achieved the target we set to reduce the highest levels of campylobacter. They have invested a lot of effort and money into interventions to tackle the problem.
"But there is more to be done and our focus now is on encouraging the smaller retailers and processors, who generally haven't met target levels, to follow the lead of the major
An M&S spokeswoman said: "We've taken action over the past two years and now have significantly more chickens that are free of campylobacter. We're ahead of the FSA target and will continue to invest to tackle this industry-wide issue."
Which? managing director of home services Alex Neill said: "It is encouraging to see that overall levels of campylobacter in chickens are falling and that major retailers are meeting the FSA's target.
"However, there is no room for complacency as the survey shows that over half of chickens are contaminated and that this can vary greatly depending on where consumers shop."