The Foreign Office said a third plane was being sent to the capital city of Juba today and warned the government would struggle to help anyone who chose to stay.
Fighting has spread through the newly formed East African state, which gained its independence in 2011, following a reported coup attempt in the capital last weekend.
British military transport planes have been used to evacuate two groups of UK nationals in recent days, but a United States rescue plane was hit by incoming fire, leaving three American service personnel wounded.
The UN has estimated up to 500 people have been killed in fighting between rival factions following a coup attempt against the president by soldiers loyal to his former deputy.
A spokesman for the Foreign and Commonwealth Office said it was sending a "third and final plane to assist any remaining British nationals to leave."
"We strongly advise all British nationals in South Sudan to leave the country if they can do so safely. You may have difficulty leaving in the event of a further deterioration in security."
The Archbishop of Canterbury, the Most Rev Justin Welby, and the Vatican called for the nation's weak and poor to be "spared the trauma of conflict". In a joint statement, they said: "On behalf of our churches we appeal to the leaders in South Sudan to lay down their weapons and co-operate in seeking peace through dialogue and negotiation."