The agency said it is conducting an investigation at the sites in Anglesey and Scunthorpe, which started last Friday with findings due to be published soon.
It has reviewed video footage and photographs of three incidents at the plants and checked it against its own records.
FSA said it was satisfied that the specific problems at the plants were addressed by the business at the time and did not present a food safety risk.
The move comes after an investigation by the UK newspaper, The Guardian, highlighted practices including chickens that have fallen onto the floor being put back on production lines.
The two factories owned by 2 Sisters supply chicken to Tesco, Asda, Sainsbury's, Aldi, M&S, KFC and to farms.
“We have been reiterating our advice to consumers that Campylobacter can occur on chickens even when the highest standards of farming and processing are followed. Consumers should follow good hygiene practice at home, including not washing raw chicken, to minimise the risk,” said the FSA.
2 Sisters and Faccenda response
2 Sisters Food Group said the allegations made in the article concerning its business and management of Campylobacter are ‘untrue, misleading and inaccurate’.
“There is no Campylobacter contamination or problems at our sites, as confirmed by multiple independent external audits and our own rigorous testing,” the firm said in a statement.
“We are doing more than any other business in addressing the key issues our sector is facing and we are leading the way in establishing and enforcing industry best practice.”
2 Sisters said it had asked the newspaper to provide the footage and details of breaches of hygiene found but it has refused to do so.
The allegations in the Guardian article were also made against an abattoir owned by Faccenda which supplies Asda and Nando’s.
Faccenda said it operates under the Red Tractor standard, and is subject to unannounced audits.
“We are investing heavily across our business to identify ways of reducing the risk of Campylobacter. In addition we have developed new innovative packaging to help food safety in the home.
“Far from being pressurised by customers, we have close trusted relationships with our partners who work with us to ensure that the public can have confidence in the food we supply.”
Unite’s inspection rights call
Jeremy Hunt, the Secretary of State for Health, ordered investigations into the issue following allegations by the newspaper which prompted the FSA action.
However, Unite the union, said that while it welcomed the call from Hunt for food inspectors to be sent into two chicken factories in the Guardian article, the need for much-improved inspection right across the industry continues.
Julia Long, Unite's national officer for the food sector, said: "We are glad that Jeremy Hunt has woken up to the importance of food inspection, but he is a bit late to this party. Where was he when we were fighting to stop cuts to the service?
"The industry needs an inspection regime that respects this and understands that public safety and confidence are paramount. At the moment, thanks to the running down of the service, a business can look forward to an inspection only once in a blue moon.
"If the government is serious about standards across this industry it must beef up our inspection services, and stop deriding health and safety protections as needless red tape."
Unite cited a 2013 FSA report which showed that of the 608,143 local authority-registered food establishments, more than 55% did not receive an inspection from April 2012 to March 2013.
The British Poultry Council issued a statement on the allegations against two of its members.
“The individual incidents shown appear to be breaches of good hygiene and manufacturing practice. They will be thoroughly investigated and corrective action taken to ensure they are not repeated," it said.
“However, they are isolated events and are in no way representative of the high standards of the chicken industry as a whole.”
- Read the results of the audit from the 2 Sisters Food Group plants here