John and Susan Cooper, from Burnley, Lancashire, died while on holiday in the Red Sea resort of Hurghada.
The couple had been staying at the Steigenberger Aqua Magic Hotel in the popular coastal destination.
Thomas Cook said the tour operator would be offering customers alternative hotels within Hurghada from Friday onwards, as well as giving them the option to return home.
A spokesman said: “We are deeply saddened by the tragic deaths of two of our customers that were staying in the Steigenberger Aqua Magic Hotel in Hurghada, Egypt.
“The circumstances of their deaths are still unclear. We have also received further reports of a raised level of illness among guests.
The Steigenberger Aqua Magic Hotel was last audited by Thomas Cook in late July 2018 and received an overall score of 96%.
“Safety is always our first priority, so as a precautionary measure we have taken a decision to remove all our customers from this hotel.”
The spokesman added on Thursday night: “For those customers who choose to come home, we have made arrangements to fly them back tomorrow, August 24. While we understand this is upsetting for those on holiday, we believe this is the right thing to do.
“We continue to work closely with the hotel and are supporting the authorities with their investigations.
“The Steigenberger Aqua Magic Hotel was last audited by Thomas Cook in late July 2018 and received an overall score of 96%.
“We will be contacting those customers due to travel to the Steigenberger Aqua Magic Hotel in Hurghada in the next four weeks to offer alternative holiday options.”
Mrs Cooper worked at the tour operator’s Burnley branch, which was closed on Thursday.
The listing for the hotel on the Thomas Cook website includes a line saying: “Sorry, there is currently no availability.”