The government has issued a salmonella warning after an investigation revealed that at least 100 people had been poisoned by British eggs in three years.

On Saturday, following the joint investigation, the Food Standards Agency (FSA) issued a food alert, warning consumers that eggs from a specific English flock could be contaminated with salmonella. The eggs in question were marked with the British Lion stamp, which is supposed to guarantee they are safe.

Salmonella can cause food poisoning, and in the most severe cases can be fatal. There have been no deaths in this outbreak. Previously the FSA had insisted British Lion eggs were safe to eat raw, even for pregnant women, children and the elderly.

It has now emerged that regulations designed to ensure high standards in the UK egg sector were breached several thousand times by farms, packing stations and wholesalers over the last three years, according to records seen by the Bureau of Investigative Journalism and the Guardian.

Inspection records have shown that more than a hundred tests for salmonella had been missed, or carried out too late, increasing the chance of contaminated eggs entering the food chain.

Over three years egg farms in England had more than 100 breaches of the rules around the government’s programme to prevent salmonella.

Some offending farms were issued with penalty notices, which can result in a fine or other enforcement action.

Dozens of people poisoned this year by salmonella-infected British eggs Read more

The records – compiled by the Animal and Plant Health Agency (APHA) – also show that one in six of all inspections carried out in the past three years found infractions on issues including hygiene, animal welfare and egg quality.

Ensuring farms are regularly cleaned and disinfected, alongside strict pest control and biosecurity measures, is key to preventing salmonella, which can be spread by contaminated wild birds and animals, in water, and via farm workers.

A single lapse in hygiene could introduce salmonella on to a farm or enable the pathogens to spread, industry sources have said.

Last week an investigation revealed how a major outbreak of one of the worst strains of salmonella had affected several farms and two egg-packing factories, including one that supplies major supermarkets.

More than 50 egg-laying flocks were found to have tested positive for salmonella since January 2018, 11 of them contaminated with the most serious strains of the bacteria. Egg-packing factories were also found contaminated on five occasions in the period.

Almost all of the 13bn eggs eaten in the UK come from British farms. More than half of the market comes from free-range hens, while most of the rest is from birds in “enriched cages” – indoor enclosures for dozens of birds with perching spaces and scratching areas.

The salmonella outbreak revealed by the Bureau is understood to have affected some free-range egg farms.

The government confirmed on Friday that it was “investigating and taking action” to control the outbreak along with industry and local authorities. In its food alert the FSA said there was a “potential but low risk of illness” and advised people to cook their eggs thoroughly to eliminate the bug.

A spokesperson for the APHA said: “All egg producers are subject to rigorous and regular inspections to ensure standards are being met and to minimise the risk to public health. If any producers are found to have hygiene breaches or fail to carry out salmonella testing, we will not hesitate to take action to bring them into compliance with our strict regulations. We prevent producers selling whole table eggs if their flocks are confirmed to have regulated strains of salmonella which endanger human health.”

The spokesman stated that the numbers of breaches cover a period of three years and take in more than 8000 inspections. “The risk of contaminated eggs being allowed into market is very small… Flock prevalence of regulated serovars (variations of salmonella) in UK laying flocks is very low, ranging between 0.09% and 0.16% in the 3 years under consideration.”

Responding to the revelations, Professor Erik Millstone, a food safety expert at Sussex University, said: “If 100 cases of salmonella poisoning from UK eggs has not been sufficient to withdraw the advice that UK produced eggs can safely be eaten raw, how many will be enough? How many people will need to get sick before the advice will be changed?”

Kerry McCarthy, a Labour MP, said the investigation served as an “urgent warning” to the poultry industry, government and consumers to avoid complacency. “While progress has been made on controlling salmonella in eggs … one case is a case too many.”

Cóilín Nunan, scientific advisor to the Alliance to Save Our Antibiotics, told the Guardian the problem was still less serious than in previous major outbreaks. “There is far less salmonella in [laying hens] than there was back in the 1980s and 1990s and it isn’t true that it was ever eradicated, but the overall threat to human health from salmonella in eggs is a lot less than it used to be. There is however a continuing problem with salmonella in poultry and other species, which continues to lead to human infections, including antibiotic-resistant infections.”

The Guardian contacted the British Egg Council for comment but received no reply.

Hygiene on farms and food safety for consumers are sensitive issues for the government at present, as difficulties over checks on livestock and farm produce are a major factor in Brexit negotiations over the Irish border, while consumers and farmers are concerned that looser trade rules after Brexit may result in imports of food from farms with lower animal welfare or hygiene standards from overseas.