Chickens are increasingly common in suburban gardens but many owners are unaware of the potential dangers of their pets.
An ESR study of faecal samples from backyard chicken flocks found more than four out of five were contaminated by campylobacter, a potentially deadly disease.
That is a higher level of contamination than has been found by studies of chickens in commercial operations.
The contamination in itself usually isn't a problem but people become infected when they ingest traces of chicken faeces, such as when hands are not washed adequately after a pen is cleaned or eggs collected. Children and elderly people are most vulnerable.
Most affected people suffer severe diarrhoea but the disease can cause permanent neurological damage and there have been at least two deaths in New Zealand.
NZ has had one of the highest rates of campylobacteriosis in the developed world, at one point 10 times higher than the United States'.
The number of cases has dropped dramatically in recent years, and has been level at about 160 cases per 100,000 people a year since 2008, about half what it was in 2006.
Auckland's regional public health service said it was told of about 1,750 cases a year but did not know how it was caught most of the time.
Rob Lake, of ESR, said the drop was due largely to intervention in the poultry sector. But while commercial operators have improved their processes, the risk remains for those who have chickens at home.
The scientists believe hundreds of people could be falling sick every year because of it, most in summer.
Many of the genotypes found in the backyard chicken flocks had also been detected in human cases, supporting the theory of pet chicken-to-human transmission.
Lake said the disease was likely more prevalent than statistics indicated because often it was not reported. Even when it was, testing was rarely done to pinpoint where it was caught.
He said people who were around backyard chickens needed to be aware of the danger. "People should be aware if they are collecting eggs that there is a risk and it's good to practice general hygiene advice, such as washing hands."
But many chicken owners are not.
Tammy Downes, of Laingholm, was not very bothered for herself or her 4-year-old daughter, Eloise.
"I just make sure she washes her hands after touching them. I tell her to be careful but that's more everyday hygiene than any specific concern," she said.
But New Lynn woman Diane Greenwood said campylobacter had crossed her mind.
"I make sure I wash my hands and I always wear footwear that's different for going into the chicken area so I'm not walking chicken poo around the place."
The ESR study showed rural flocks, on farms and lifestyle blocks, tended to have more varied genotypes of campylobacter than urban flocks.
Heather Lowrie, who runs a business called Backyard Chooks, which sets people up with chickens and coops, said there was a lot of interest in pet chickens and people should not be put off by the reports.
"There's a protective coating on the eggs. You don't need to go too overboard trying to clean and sterilise them. Just be careful to keep rotating them so they're fresh."