The travel giant revealed the results of independent tests conducted at the Steigenberger Aqua Magic Hotel that showed the presence of the food poison bug – as well as bacteria linked to deadly toxic shock syndrome.
Experts analysing food and hygiene standards at the resort identified a high level of e-coli and staphylococcus bacteria.
But Thomas Cook insists the results do not shed "any light on the still unexplained cause of death" of British holidaymakers John and Susan Cooper.
The couple, from Burnley, Lancs, died within hours of each other at their Hurghada resort on 21 August.
Their deaths were initially recorded as being down to heart and respiratory failure — but a postmortem is due to be carried out.
John, 69 died in his room after collapsing on his bed, while wife Susan, 64, was rushed to hospital but later succumbed to the mystery illness.
Thomas Cook's commissioned an independent hygiene specialist and air quality specialist to test the hotel amid fears they may have come to harm through the air conditioning food or water.
Reporting the results today, the company revealed:
There was no evidence of carbon monoxide and normal levels of carbon dioxide in and around the Coopers' hotel room
Tests on the swimming pools showed normal levels of chlorine
The tests did not identify the presence of shigella, listeria or salmonella
But tests on the food and hygiene standards identified a high level of e-coli and staphylococcus bacteria — which can cause blood poisoning and toxic shock