The health secretary, Jeremy Hunt, intervened in the row over food hygiene on Thursday demanding that the Food Standards Agency mount an urgent investigation into the processing factories at the heart of a Guardian investigation into contamination in the poultry industry.

A safety audit will be carried out within 24 hours at two factories identified by undercover footage, photographic evidence and information from whistleblowers. The evidence showed how strict industry hygiene standards can be disregarded in practice, potentially encouraging the spread of the bacterium campylobacter, which contaminates two-thirds of fresh retail chicken and can cause food poisoning and, in rare cases, death.

On Thursday the FSA initially promised to investigate the evidence but rapidly said it was "content" with the way the official vet at the chicken processing plant and the company had dealt with incidents.

Within hours, however, at Hunt's request, the FSA confirmed it would send auditors in almost immediately and that they would be reviewing CCTV of activity on the factory floors. "We don't think there was a risk to public health from the evidence we've seen, but we want to do a full safety audit," the FSA said.

A spokesperson for Hunt said: "The FSA has agreed, at the request of the secretary of state for health, to conduct a full safety audit of the facility. They will start in the next 24 hours and report back shortly."

The government has separately been considering proposals to reduce the contamination of fresh chicken with campylobacter by spraying carcasses with acid or flash-freezing their surfaces after processing. In an admission that other measures to clean up the industry have so far largely failed and that most chickens remain contaminated, the FSA has looked with the poultry industry at technical fixes to kill the bacteria at the end of the chain before chickens go on sale.

Chris Elliott, professor of food safety at Queen's University Belfast, said that most interventions had been ineffective. Campylobacter contamination would continue through the farming, slaughtering and cutting chain, and would have to be tackled with new chemical or freezing processes.

Carcasses are already sprayed with lactic acid in the US, where contamination levels have typically been high. Elliott said there would be strong consumer resistance to fresh chicken undergoing a chemical process in the UK, although research suggests it is safe. Lactic acid and antimicrobial sprays are not permitted on poultry in the EU.

"Campylobacter is a very, very difficult organism to control and what's happening in the UK is matched everywhere else in the world. The industry will have to tackle this at the processing stage and it will need sizable investment in plant [machinery]," Elliott said.

Another technique involves flash-freezing the surface of chickens using liquid nitrogen to kill the bacteria. Trials by two of the largest UK poultry processors, Bernard Matthews and Faccenda, have shown this reduces campylobacter levels by around 90%, but introducing it for all production would require investment in machinery and increased running costs. EU regulations prohibit the sale of meat that has been frozen in any way being labelled as fresh but the FSA believes flash-freezing to minus 2 degrees celsius would meet the regulations.

At the last count two thirds of fresh chicken was found to be contaminated at varying levels by campylobacter. Although the bug is killed by cooking, around 280,000 people a year in the UK are made ill by it, and it is thought 100 die. Poultry contamination rates are known to have increased in the past decade.

The Guardian's investigation involved two factories owned by the UK's largest poultry supplier, 2 Sisters, which supplies major restaurants and supermarkets – three of which have already launched their own investigations. The factories are in Scunthorpe, Lincolnshire, and Llangefni, Anglesey. Evidence documented repeated breakdowns that led to guts, offal, and feathers – all high-risk material for campylobacter – piling up on the factory floor while production continued. Sources described a scald tank, through which chickens pass before plucking, not having its water changed for days.

Undercover footage at another factory showed chicken that had fallen on to the factory floor being picked up and thrown back into the production line. 2 Sisters denied that chicken is ever put back into production from the floor and said it is always disposed of correctly as waste. It said it did not stop the line when offal, guts and feathers were piling up because it had to consider the welfare of chickens waiting in crates to be killed. The incident with water not being changed in the scald tank lasted only one day, it said, and bacteria counts were checked and were acceptable.

Labour accused the government of "presiding over another food scandal".

Huw Irranca-Davies, the shadow food and farming minister, said: "These are serious accusations of malpractice in the poultry slaughter and processing sector. If it is found that consumers have been put at risk we would expect swift and strong action to be taken to restore public confidence, including action against individuals and companies if appropriate."

Irranca-Davies wrote to the chief executive of the FSA, Catherine Brown, expressing concern that the agency's initial inquiries had been cursory and seeking assurance that it would conduct a fuller investigation and publish the results.

He also asked whether any conversation with Downing Street had influenced the FSA's decision, endorsed by a divided board yesterday, to break its promise to name and shame individual supermarkets and chicken factories in quarterly reports on testing for their campylobacter counts. The FSA said as recently as March that it would show "steely determination" in standing up to industry opposition to naming and shaming.

• Read the full responses of the poultry industry here

• This article was amended on 28 JUly 2014. An earlier version said trials by two UK poultry processors had shown a flash-freezing technique reduced campylobacter levels by around 10%. That has been corrected to 90%