Thomson and First Choice, which are owned by London-listed TUI Travel, Europe's biggest tour operator, said they had also decided to cancel all flights to the coastal city until November.
Britain's Foreign and Commonwealth Office (FCO) warned on Wednesday against "all but essential" travel to Mombasa, citing "recent terrorist attacks and the continuing terrorist threat in the area"
"As a result of the change in FCO advice, the decision has been taken to cancel all our outbound flights to Mombasa, Kenya up to and including 31 October," Thomson and First choice said in a statement.
A spokeswoman told AFP that Thomson and First Choice had around 400 customers currently on holiday in Mombasa.
"Some arrived home on a flight home this morning, some will arrive on a flight this evening, and the rest on Monday," she said.
Britain's Foreign Office said it was not involved in pulling tourists out of the area.
"We are not assisting with the evacuations, it is entirely down to the travel companies," a Foreign Office spokeswoman told AFP.
Australia and France also updated their travel advice for Mombasa this week.
Kenya has been targeted by Somalia's Al-Qaeda-linked Shebab rebels since it sent troops to war-torn Somalia in 2011 to fight them, and it suffered a major blow in September 2013 with the deadly attack on the Westgate shopping mall in Nairobi.
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