The travel agency said safety is always the first priority, and have made a decision to move all customer from the hotel as a precautionary measure.
Others said Thomas Cook has not provided sufficient explanation for the evacuation arguing that other travel agencies have not taken such an extraordinary step.
Thomas Cook said in a statement Thursday that the circumstances surrounding the deaths remain unclear but that it had received reports of "a raised level of illness among guests".
The hotel said on Friday that there had not been a rise in cases of illness.
The sudden deaths on Tuesday of John and Susan Cooper prompted their travel company to evacuate all of its guests in the hotel on Friday, amid a welter of conflicting accounts from guests, managers and Egyptian officials about what led to the couple's demise.
Carol Mackenzie, Thomas Cook's head of customer welfare, told Sky News she flew out to provide support to the family affected by the deaths.
"I went to hospital in the ambulance with mum where she passed away", she said.
A health inspector examined Cooper's body "and documented in his report that the cause of death is the halt of the blood circulation and her respiratory functions, and that there was no criminal suspicion", according to the tourism ministry. Hours later his wife, 64, is taken to a hospital where she, too, dies.
South Africa summons US official over Trump tweet
South Africa's has long attempted to right the wrongs of apartheid in its country, owning up to its racist past. South African President Cyril Ramaphosa speaks in parliament in Cape Town, South Africa, February 20, 2018.
Janine Traviss, from Oldham, England, said she and her partner contracted a stomach bug earlier this month.
"We have no cause of death, a post-mortem is under way".
"The Steigenberger Aqua Magic Hotel was last audited by Thomas Cook in late July 2018 and received an overall score of 96%".
He added: "The doctor's preliminary report indicates that death was due to natural causes".
"We spoke to the reps throughout the whole time we were there about why we were poorly - if it was because of food poisoning or the air conditioning", she said.
The listing for the hotel on the Thomas Cook website includes a line saying "sorry, there is now no availability".
Mr Fankhauser continued: "Twenty-four hours after the couple died, we had our specialists.in the hotel".
The Foreign Office said in a statement: "We are supporting the family of a British couple who died in Hurghada, Egypt and we are in contact with the local tour operator".