At least 53 people are known to have come down with severe stomach upsets after contracting salmonella montevideo, a rare strain of the disease.

This weekend the Health Protection Agency (HPA) confirmed molecular fingerprinting tests had shown that the bacteria that caused the outbreaks were the same as those contaminating some of its products. Last week the company, Britain’s biggest chocolate manufacturer, recalled 1m chocolate bars.

The HPA said the number of cases of the disease could be up to five times higher than the 53 reported because many people with stomach upsets never visit their doctor.

“The molecular typing showed that the samples from Cadbury were the same as the human cases. We cannot be 100% sure that Cadbury’s products caused the disease but it is a strong possibility,” said the HPA.

This weekend Cadbury, which sells £1 billion worth of chocolate a year, was also accused of failing to follow key food safety principles.

Following the initial alert that became public on Friday, the company has repeatedly insisted that low levels of salmonella in ready-to-eat foods are harmless and acceptable.

However, microbiological experts and official agencies said high levels of fat and sugar in chocolate made it an ideal vehicle for preserving salmonella and carrying it into the intestine. This meant that serious illness could be caused by what appeared to be mere trace levels of the bacterium.

The Food Standards Agency (FSA), the government’s watchdog, said: “Salmonella is unacceptable at any level and we would have expected Cadbury to have notified us far earlier than they did on finding this bacterium in their products.”

The contamination was first detected in January in chocolate at the company’s Marlbrook plant in Herefordshire. The plant produces nearly 100,000 tonnes of chocolate crumb a year, which is sent to other factories to be mixed with cocoa butter and made into chocolate products.

The company said the contamination was traced to a leak in a pipe carrying waste water from cleaning machinery that was dripping on to the floor near a conveyor belt. Cadbury said the pipe was fixed at that time, so ending the problem.

However, this explanation raises several questions as the HPA said up to eight subsequent samples taken from January to June also showed contamination.

Cadbury sent the initial and later samples to an independent laboratory for testing. The laboratory told Cadbury that the samples contained salmonella and then sent them on to the HPA to find out the exact strain, but it did not tell the HPA the origin of the samples.

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