The travel company had re-introduced holiday packages and flights to the destination in its line-up earlier this year, amidst hope that the threat levels would desist, but with no change in the foreseeable future the holidays have been cancelled.
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However, it's not all bad news for holidaymakers who have already booked into the packages and flights - the company is offering its customers a choice of alternative holidays, or if preferred, a full refund.
Although Sharm El Sheikh still appears as a destination on the Thomas Cook website, there is no option to book in to any holidays or flights.
The page does however include an explanation from the company as to what prompted the decision.Empty sun lounges on a beach in the Egyptian Red Sea resort of Sharm el-Sheikh
"We have removed Sharm El Sheikh in Egypt from our Winter 2017/18 and Summer 2018 holiday and flight programmes," reads the statement. "The UK Foreign and Commonwealth Office continue to advise against travel to Sharm El Sheikh airport, and we have no plans to reintroduce a programme to Sharm until after that advice changes.
"The five flights per week which we had scheduled this winter have now been cancelled.
"We are contacting those customers who have booked with us to offer a refund or a destination change free of charge. Your safety is our number one priority."British passengers wait to check in at the airport of Sharm el-Sheikh, Egypt
Travel to the Egyptian resort was first suspended in December 2015, after the bombing of a Russian passenger plane killed 224 people.
Following the incident thousands of British passengers were left stranded for weeks after airlines including easyJet and British Airways cancelled their flights to Egypt.
Since then, the Foreign Office has continued to warn against all but essential travel by air to the area.
You can see the full travel advice from the Foreign Office regarding Egypt on their website here.