Cook agent Susan Cooper and her husband John fell fatally ill while staying at the Steigenberger Aqua Magic hotel in Hurghada last month.
In an official statement, Prosecutor Nabil Sadek said post-mortem examinations showed E. coli bacteria to be the cause of the death, the BBC reports.
The Evening Standard said the tests showed Mr Cooper suffered acute intestinal dysentery caused by E. coli, and Ms Cooper suffered Hemolytic-uremic syndrome (HUS), likely also because of E. coli.
Sadek added the couple’s bodies showed "no criminal violence" and other tests on air and water at the hotel found nothing unusual.
Cook’s own tests found a high level of E. coli at the hotel, but said the tests - which it had independently verified in London - didn’t shed any further light on the couple’s death.
Thomas Cook commented: “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 21 August 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.”