John and Susan Cooper died in their room at the Steigenberger Aqua Magic Hotel in the Red Sea resort of Hurghada.
Daughter Kelly Ormerod, 40, slammed the UK over their delay in finding out what had killed her parents.
She told The Sun: “I do think that my parents’ bodies are missing body parts but I am getting no answers.
“I have been led to believe certain organs are missing.
“I feel it is being covered up.”
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Thomas Cook has confirmed high levels of E-coli were found in food at the hotel where the couple died.
The travel company revealed the results of independent tests conducted at the Steigenberger Aqua Magic Hotel.
The tests showed the presence of E-coli and staphylococcus bacteria in the food, as well as bacteria linked to sepsis and deadly toxic shock syndrome.
Thomas Cook is adamant the results do not shed “any light on the still unexplained cause of death” of the Coopers.
John and Susan died within hours of each other.
Their deaths were initially recorded as being down to heart and respiratory failure.
A spokesman for Deutsche Hospitality, which runs the hotel, said: “We are deeply saddened by the tragedy in the Aqua Magic Hotel in Hurghada.
“We are expecting the results of the full investigation being conducted by the Egyptian authorities, who have our full support.
“We are constantly monitoring the quality by outside independent contractors.
“So any high level of bacteria would not be acceptable by our high standards.
“We have taken note of the interim results published by our partner Thomas Cook, which matches with our independent investigations concerning the good results of water and air quality.
“Our high standards in terms of hygiene are not negotiable and of course apply also to all of our franchise hotels as well.”
Thomas Cook chief executive Peter Fankhauser added: “These results, while not establishing the cause of the tragic deaths of John and Susan Cooper, have prompted us to commit further resource to tackle hygiene standards in those hotels where we identify a higher than average level of sickness.”
A Foreign Office spokeswoman said it was assisting the Cooper family.
She said: “We continue to convey requests from the family and the UK coroner to the Egyptian authorities.”
This comes after the body of David Humphries was returned to the UK from Egypt with no heart or kidneys.