This week it was suggested that the growing numbers of city dwellers keeping chickens were spreading disease and harming birds. But is it just bad blood on the part of big food producers?

Billy, seven, brings me a book. "Have you seen this?" It is a well-worn copy of Keeping Chickens, with colour photos and illustrations on every page, several of them featuring attractive children shot against beautiful blue skies. On the table in the open-plan living space of his north London family home, the book falls open on a chapter headed "What to consider".

"Ask yourself whether you are interested in keeping chickens for profit, self-sufficiency, or purely for pleasure," go the instructions, before advising readers to check with neighbours and the local authority before going ahead. If bylaws don't allow chickens in the garden, "think about moving house".

Billy's parents, Jon and Lindsay, have five chickens. There were six until a month ago – one for each member of the family – but then a fox came and killed Sandwich, who belonged to three-year-old Josie, by climbing into the hen house when Jon's back was turned. The other chickens haven't been the same since. When the fox came back to finish its meal, he chased it off with a spade.

The Rogers family bought their chickens earlier this year, having seen some at someone else's house and thought "ooh what a lovely idea!" They drove up all together to a small farm near Watford, and paid £16 each for the birds. Enid, Jessie and Beryl were named after relatives. Kentucky was teenager Kiran's idea. Billy's chicken, Gwen, is named after Ben 10's cousin from the cartoon.

They have found keeping chickens harder than expected. They had to phone the farmer the first evening for advice on how to get them into the hen house. Then they had an infestation of red mite, traced to the second-hand coop they bought on the internet. The tiny parasites get all over everything and make humans as well as birds itch, but when they bought a new £150 hen house, things settled down.

Jon, who runs a mail-order business from an office at the bottom of the garden, says the summer was great. "I'd let them out for the whole afternoon to run around. You do get quite attached to them. Intelligent is probably the wrong word, but they do recognise you, and have slightly different personalities. There's something nice about going to the coop and getting the first egg in the morning. It's about as close to 'the good life' as you could get really without having Jerry and Margot next door." As he talks he reaches in, fishes out an egg and hands it to me – still dirty and warm.

The Rogers family are members of a growing army of urban grow-your-own enthusiasts that has moved on, over the past decade, from growing beans and strawberries to keeping chickens and even bees. But in recent weeks such amateur, household-scale food producers have come under attack.

This week newspapers reported on research from the Royal Veterinary College suggesting backyard chicken-keepers in the Greater London area risk spreading illnesses such as Marek's disease, Newcastle disease and infectious bronchitis, and causing children to get diarrhoea. Last month potato growers were blamed for worsening an outbreak of potato blight by failing to dispose of infected potatoes. Allan Stevenson, chairman of the Potato Council, told trade journal The Grocer that "it would be preferable if people bought healthy, well-produced potatoes from their retailer rather than grow their own".

But are such attacks justified? Duncan Priestner, an egg producer with 120,000 indoor-reared birds in south Manchester, and chairman of the National Farmers Union poultry board, says there are real fears that more outdoor birds in more places could mean more diseases. "With an outbreak of bird flu there is a surveillance zone [in which movement of birds is restricted] of 3km, so if one person got bird flu it could shut down a big commercial unit. From a farming perspective, the fewer birds the better, really. My ideal situation would be for nobody else to have any birds for three or four miles around. But, of course, we live in the real world, and people have every right to keep chickens."

Vet Victoria Roberts, a poultry specialist who runs training courses and advises hobbyists in Your Chickens magazine, says the industry is "terrified backyarders are going to introduce some terrible disease.

"They thought it was going to happen with the avian influenza in 2007, but then when the virus was found, it was in an industrial unit." She adds that "keeping hens outside rather than inside obviously exposes them to parasites and certain diseases. But on the whole they are easy to keep, and great fun as long as people observe some practical hygiene".

There is broad agreement that some people should not be keeping chickens. Pullet breeder Andy Cawthray has sent some people away with a magazine or a book. "People need to go into it with their eyes wide open – don't go and buy a handful of fluffy chicks for your daughter because you think they're cute."

There are some amateur breeders or "sharks" out there who don't vaccinate their birds, says Roberts. She suggests Defra (the Department for Environment, Food and Rural Affairs) should think about registering all chickens – not just flocks of more than 50, as at present. But she and Cawthray are united in defending the vast majority of chicken-keepers against the suggestion that they may be doing more harm than good.

Both point out that the sample size for the research was very small. Just 30 chicken-keepers out of 65 who had volunteered turned out to be suitable, and the survey was carried out in 2010. "It doesn't really stand up under research rules," says Roberts. Barbara Haesler, one of the study's authors, says it provides a starting point. "Research in this area is incredibly limited. We don't have any baseline data or know how many chickens there are in London. So it gives an indication of what is going on."

Some of the tension arises from whether poultry are viewed as livestock or as pets. Chicken-keepers admit to mixed emotions when confronted with sick hens, and learning to kill them humanely is not easy. Just like dog and cat owners, many of them love their birds, treating them as part of the family and referring to them as "the girls".

Charlotte Popescu, who keeps chickens in Wiltshire and wrote one of the first how-to books in 2003, says: "It's addictive. You have two or three chickens, and they lay for two or three years and then you think, should I get more?"

Julia Hollander, another author who keeps hens in her Oxford garden and allotment, says: "To me, they make a home. I wouldn't want to be reckless in the face of warnings, and I'm sure there are stupid people out there who don't realise animals need looking after. But it's a positive side of the recession that there's this whole back-to-basics thing. Eggs have gone up a lot in price, and chickens cost £6, so once you've got a coop you may as well carry on."

Others agree what might begin as a hobby can morph into a self-sufficiency drive – particular as concerns about rising food prices and long-term food security gain ground. Mainstream pet shop chain Pets at Home has joined specialist suppliers and garden centres in selling feed and supplies, and even sells chickens in one London store.

"I love being able to dig up a carrot or a potato when I need one. I don't have to go to any shops," says Popescu, who grows vegetables in a cage to protect them from the chickens, but lets them in once she has dug up the crops, for their manure, and so they eat the slugs. "I've got carrots out there, beetroots, jerusalem artichokes. My whole diet comes from the garden. Often I just eat some kind of egg with the vegetables."

So do these recent stories reflect a deeper antagonism between Britain's commercial food producers and their amateur city cousins, who buy organic when they can? Green groups such as the Transition Network have become energetic advocates of locally grown and sourced produce. The grow-your-own movement is linked to the huge expansion of farmers' markets over the past decade, as well as the calls for better labelling by supermarkets, better deals for small farmers, and greater awareness of food miles. This summer even Michelle Obama published a book about the White House vegetable patch.

Many people are by now familiar with an argument about food that pits quality against cost, with assorted campaigners including Jamie Oliver and Hugh Fearnley-Whittingstall challenging the might of the food industry in an attempt to prove that, when we think about how we eat both now and in future, there must be considerations other than price.

Chicken enthusiasts complain it is big industrial farms that mistreat animals, that the rescued battery hens some people now take in as pets are visibly distressed. Cawthray says, "the question is not the health threat to the poultry industry from the back yard. It's the other way around."

The NFU counters that feeding kitchen scraps to chickens, as some home chicken-keepers undoubtedly do, is illegal. What might seem like wholesome recycling to a well-intentioned amateur could actually spread disease.

Wilfred Emmanuel-Jones is one farmer, with a previous career in TV, who has highlighted the breach between town and country, which he believes is more extreme in Britain than anywhere else. "There are many in the farming establishment who roll their eyes at the idea of city types keeping animals," he says. "Someone keeping a dozen chickens is nothing to get cross about. They should be praised and encouraged."

But while parts of the media surely had Guardian-reading, organic celeriac-eating, innercity do-gooders in mind when they reported on the damage that could be caused by London's newfangled chicken-keepers, sometimes the politics of food are less clear-cut. Priestner says the vast numbers of game birds bred in the countryside for shooting, primarily pheasant and partridge, are more of a worry to industrial farmers than are a few urban hens, in terms of disease.

Meanwhile, city chicken-keepers, once they have lost a hen to a fox, find they have more in common with fox-hating farmers than they thought they did. "I didn't really mind foxes before the chickens," says Jon Rogers in his garden in Crouch End.

London primary schools and at least one prison now keep chickens. Because there is no register, no one knows exactly how many chicken-keepers there are nationally, but experts suggest the number could be as high as 750,000.

Whether they all keep it up remains to be seen. When the Rogers family move house next year, they may stop. "They do produce an awful lot of mess," says Lindsay. "I've never seen so much shit. They produce a giant bin bag a week, I would say. You can have too much compost, if you know what I mean."