A contractor told the BBC he warned in 1998 that refurbishment work at its London Marble Arch store was breaching asbestos removal guidelines.
In 2011 the company was fined £1m over work at its Reading store.
The company said it carried out a full investigation into the Marble Arch work and no-one was put at risk.
William Wallace, who was working as a health and safety manager, wrote his letter to the then chairman of the company, Sir Richard Greenbury, after what he says were a series of breaches at the London store, recorded in the logs left between shifts.
‘Safety not guaranteed’
One report from April 1998 described how cladding had been stripped with a sledgehammer and asbestos was “everywhere” .
The nightshift workers recorded that it was the “third occasion in a week” they had had to clean up after a “dangerous occurrence”.
Later one contractor described how he should “legally report” more instances of broken asbestos being left lying around.
Mr Wallace told the BBC’s Inside Out programme: “There were minefields, asbestos minefields for the want of a better expression.
“You could not have guaranteed the safety of anybody, the workers, the staff, the customers: you could not have given a 100% guarantee that those people were safe.”
Mr Wallace said he set out his concerns in a letter to Sir Richard and three days later met senior managers and showed them copies of the log. He was promised there would be a full investigation.
Steve Rowe, a Marks & Spencer board member, said: “On the face of it these allegations sound worrying, but our team at the time 15 years ago thoroughly investigated them on the day.
“They thoroughly investigated them some three months afterwards and again I’ve spoken to those individuals and could find no case whatsoever to say any member of staff or any member of the public was put at risk.”
But in 2006 Mr Wallace said he was again concerned by what he saw – this time at the Reading store as it was being refurbished.
The Health and Safety Executive later took the company to court.
One witness who gave evidence has spoken to the BBC. He asked not to be identified for fear of being blacklisted by the building industry.
The witness – a construction worker – told the court he was overruled by Marks & Spencer managers after he ordered that fans in the ceiling void should be turned off to avoid circulating dust which might contain asbestos.
The witness told the court he returned to work to find the fans had been turned on again, on the instruction of the Marks & Spencer managers, to prevent food refrigerators overheating.
On another occasion he described how he saw dust from the ceiling falling on a shop assistant stacking sandwiches. Construction workers warned her to move.
He said: “The night manager responsible for the refilling of the shelves came and went absolutely ballistic at us, and told us that we don’t tell his staff where to go and he sent her back to go and fill the sandwich (shelves) which at that point would be covered in asbestos dust.”
Imposing the £1m fine plus costs, Judge Christopher Harvey Clark said there had been a “systemic” failure by Marks & Spencer management and its response to asbestos safety complaints was to “turn a blind eye” to what was happening because the asbestos work was “already costing the company too much”.
‘No blind eye’
The judge said that contractors, staff and shoppers “have a right to be anxious as to whether they have breathed asbestos fibre and what effect that might have on their well-being and future”.
Marks & Spencer continues to describe the judge’s comments as “disappointing”.
Mr Rowe told the BBC: “Marks & Spencer never, ever puts profit before safety.
“There wasn’t a blind eye. Our investigations were full and thorough.
“We have a very good policy which the judge described as sensible and practical.
“Implementation of the policy wasn’t good at Reading. We are very sorry about that. We regret it. So we are disappointed by the judge’s comments.”
Stores other than Marks & Spencer have also been fined for asbestos breaches, including House of Fraser in 1997 by Birmingham magistrates, Blacks in London for an incident in 2005, the Co-op, Manchester in 2007, Top Shop, Liverpool in 2008 and John Lewis, Edinburgh, also in 2008.