The ship will instead be based in Limassol for the rest of this season, before moving to its new home port of Malaga, Spain, in March next year. Passengers are being advised.
The announcement comes just one day after Egypt announced it was confident that cruise lines would return to the country in 2014.
A statement from Thomson reads: “Thomson Cruises has regretfully taken the decision to cancel the Thomson Majesty Red Sea cruises scheduled for this winter.
“The safety of our customers is always our number one priority, and as the Foreign and Commonwealth Office (FCO) has advised against all but essential travel to Cairo and Luxor this means that we are not able to offer our customers an alternative itinerary that would meet their requirements for a Red Sea cruise.
"In addition, we are not able to offer the full excursion programme, such as famous sites of The Pyramids and Valley of the Kings that we know they want to experience."
Thomson is one of many cruise lines which have cancelled port calls to Egypt over the past few months. However, it was the only line to base a ship in Egypt, so its decision to cancel its winter season will come as a huge blow to the country, which has seen relative calm descend on it in the past few weeks.
Yesterday, at the U.K.'s biggest trade show, World Travel Market, Egypt's Tourism Minister Hesham Zaazou said at a press conference: “I have had a lot of talks with the major cruise operators, and I believe they will come back to Egypt in 2014.”
Mr Zaazou described the affects on tourism of the unrest which has gripped his country as “catastrophic” but sought to reassure that Egypt was safe to travel to -- despite a number of travel warnings still in place.