The Food Standards Agency said that almost one in ten chickens tested at Lidl were highly contaminated with the food poisoning bug campylobacter.
More than 1,000 whole fresh chickens were surveyed during January to March by food safety chiefs to detect for the bacteria, the main cause of food poisoning in Britain.
Marks & Spencer had the lowest levels of samples testing positive at 2.5 per cent with Morrisons and Waitrose, 2.8 per cent and 2.7 per cent respectively, also performing well.
The survey found that 3.8 per cent of the chickens sold at Tesco were contaminated, 4.3 per cent at the Co-op, 5.5 per cent at Aldi, 7.3 per cent at Asda and 7.7 per cent at Sainsbury's.
However, the number of chickens that test positive for high levels of contamination had dropped from 9.3 per cent to 6.5 per cent from the previous year.
Lidl chiefs said they were disappointed with the findings and claimed that the results had a "large disparity" from tests conducted by themselves.
A Lidl spokesperson said: "We continue to address campylobacter reduction as a priority within the business and remain committed to exploring methods with our suppliers to further minimise levels, whilst ensuring that all packaging of raw chicken includes clear labelling advising customers of the correct cooking and handling techniques to avoid cross-contamination."
But smaller retailers and butchers, classified as "others", had a significantly higher level of contamination at 16.9 per cent compared to the major supermarkets.
FSA chairwoman Heather Hancock said: "It is good to see that levels continue to go down as this indicates that the major retailers and processors are getting to grips with campylobacter.
"While the results are reassuring, we want to see more progress among the smaller businesses, to achieve real and lasting reductions.
"In the meantime, I am delighted to see the commitment and responsibility that the industry has shown, so far, in their efforts to provide consumers with food they can trust. They have invested a lot of effort and money into interventions to tackle the problem and it is showing clear results."