The chicken factories at the centre of revelations over food poisoning contamination were checked by UK Food Standards Agency inspectors on Friday, as sources reported that Tesco auditors had found failings during a surprise middle-of-the-night inspection at an abattoir in Wales.

This week’s Guardian investigation prompted emergency reviews by three of the UK’s leading supermarkets, and the health secretary, Jeremy Hunt, intervened on Thursday to demand that the FSA investigate more thoroughly, just hours after the agency had said it was content that correct procedures had been followed.

Labour accused the government of presiding over a food scandal made possible because David Cameron had split responsibility for food policy between the FSA, the Department of Health, and the Department for Environment, Food and Rural Affairs (Defra), and called on him to review the changes.

Undercover footage, photographic evidence and information from whistleblowers revealed how strict industry hygiene standards to prevent the contamination of chicken with the potentially deadly campylobacter bacterium can be flouted on the factory floor and in farms. Two-thirds of fresh chicken on sale in supermarkets is contaminated with the bug and 280,000 people a year are made sick by it.

The Guardian understands that Tesco auditors arrived unannounced at 4.30am last Friday at the Llangefni chicken processing site in Wales owned by the 2 Sisters group, after the Guardian had approached the retailer with a series of allegations about hygiene failings at this and another factory. The site supplies several leading supermarkets and fast food chains.

The alleged failings included repeated breakdowns that had led to feathers, guts and offal – high-risk material for the spread of campylobacter – piling up on the factory floor for hours while production continued. Sources also said water in scald tanks, through which birds pass before plucking, was not cleaned for three days. Whistleblowers and an undercover reporter said carcasses that had fallen on the floor at this site and another owned by the same company in Scunthorpe were sometimes recycled back on to the production line.

The company denied this, saying all carcasses from the floor were disposed of as waste. It also said it did not stop the slaughter line when the evisceration and defeathering blockages occurred because it had to consider the welfare of chickens waiting for slaughter. It said that the scald tank incident was isolated, had only lasted one day, and tests have confirmed that bacteria counts were acceptable.

Sainsbury’s and Marks and Spencer confirmed they were customers of the Welsh factory and had carried out inspections, with M&S auditors arriving unannounced last Wednesday. The Guardian understands the Scunthorpe factory has also been audited by retailers, and government inspectors arrived there on Friday.