The independent sector is trailing the big supermarket chains when it comes to ensuring chicken is free from campylobacter contamination, the Food Standards Agency (FSA) has warned.

The UK survey of campylobacter contamination in fresh chicken at retail, covering August 2016 to July 2017, shows Morrisons, Tesco and Waitrose scored best, with a prevalence of 2.9%, 4.2% and 2.7% respectively.

The “others” grouping, which comprises smaller retailers and butchers, had a 17.1% higher prevalence than the average among the nine retailers with the biggest market shares, which had a 5.6% prevalence.

The FSA tested 3,980 chickens and found, on average, 6.5% of chickens tested positive across the entire market for the highest level of contamination – down from 19.7% in 2014/15 when the survey began. The survey found a significant fall in the percentage of chickens positive for campylobacter at any level – down from 73.2% in 2014/15 to 54% this time.

Foodborne campylobacter is the biggest cause of food poisoning in the UK says the agency, which has been testing chickens for campylobacter since February 2014 in a bid to tackle the problem.

Heather Hancock, chair of the FSA, said: “The full year’s results from our third annual survey show the significant progress the industry has made in reducing campylobacter levels in chicken, compared with their starting point.”

She said that the top nine retailers would from now on publish their own results on their consumer website, according to an agreed protocol, which she described as “a welcome step towards greater transparency”.

She added: “Whilst we will keep a close eye on the performance of bigger retailers, it means the FSA can now focus our efforts on smaller establishments, where we haven’t yet seen the same level of improvement and where more progress needs to be made.”