The pair died while on holiday with their daughter and family on Tuesday, August 21st, at the Steigenberger Aqua Magic Hotel in Hurghada, Egypt.
Their daughter Kelly Ormerod found her father dead in the couple’s bedroom and was with her mother when she died several hours later.
In an official statement, the Egyptian general prosecutor said post-mortem examinations showed E. coli bacteria was the cause of the death.
Susan worked at the Burnley branch of Thomas Cook travel agents and husband John was a well-known builder in the area and owned his own company, Safe As Houses.
The couple's daughter, Kelly Ormerod, told the BBC she believes the claims of E. coli were "absolute rubbish".
She said she did not believe the symptoms her parents showed were consistent with E. coli infection.
Thomas Cook has also released a statement.
A spokesman for the company said: “Thomas Cook notes the announcement today by the Egyptian prosecutor on the results of the autopsies of John and Susan Cooper following their deaths at the Steigenberger Aqua Magic in Hurghada on August 21st 2018. We have not yet seen the full report and we will need time for our own experts to review it.
“We are deeply saddened by the tragic deaths of John and Susan Cooper. We will continue to offer every support to their daughter Kelly and the rest of their family.”