Campylobacter is the most common bacterial cause of food poisoning and is responsible for around 55,000 cases of illness in the UK every year, the agency said.
It stressed that cooking chicken thoroughly would kill the bug, and urged consumers to take simple steps to avoid cross contamination with other food products.
Andrew Wadge, director of food safety at the FSA, said: “The continuing low levels of salmonella are encouraging, but it is disappointing that the levels of campylobacter remain high.
“It is obvious more needs to be done to get these levels down and we need to continue working with poultry producers and retailers to make this happen.
“Other countries like New Zealand and Denmark have managed to do so and we need to emulate that progress in the UK.”
As part of the FSA’s work to reduce levels of campylobacter in UK-produced chicken, an international conference on campylobacter is being organised for 2010, where a range of options for tackling the bug will be discussed.
British Poultry Council chairman Ted Wright said: “The BPC welcomes the FSA’s study, which again confirms the very low prevalence of salmonella on chicken at retail sale.
“The results for campylobacter however, really confirm that there is still much we do not know scientifically about this organism, not least the difficulty in measuring its presence or absence.
“It is disappointing that the FSA has again changed the basis of the survey part-way through, making results incomparable with the previous FSA survey and with the previous prevalence estimate.
‘We need to concentrate on finding effective measures to prevent infection in flocks and less on targets that we cannot measure yet with confidence.”
He added that the BPC and the FSA were working to implement actions from scientific projects already carried out and to promote further study on the gaps in knowledge on the subject.