But the firm insisted the discovery of E. coli and staphylococcus bacteria does not reveal what caused their deaths.
Tests were carried out at the hotel but not inside the Coopers’ bedroom, as it remains under the control of the Egyptian authorities.
And the independent specialists who carried out the tests do not believe that these results “shed any light on the still unexplained cause of death of Mr and Mrs Cooper”.
Examination of air and water quality “came back clear” and there was no evidence of carbon monoxide, with normal levels of the gas in the vicinity of the Coopers’ room.
Thomas Cook said: “It is clear from these results that something went wrong at the Steigenberger Aqua Magic Hotel in Hurghada and that standards fell below what we expect from our hotel partners.
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“It is likely that the presence of E. coli and staphylococcus would explain the raised level of illness reported among guests at the hotel during this time, supporting Thomas Cook’s decision to remove our 300 customers.”
Chief executive Peter Fankhauser said: “Everyone at Thomas Cook is deeply saddened by the tragic deaths of John and Susan Cooper.
Susan [who worked at Thomas Cook in Preston] was a long-standing and much-loved colleague of ours.”