Foreign affairs issued an advisory Saturday evening saying Canadians in the African country should leave and is advising Canadians not to travel there.
"You are urged to leave now by commercial means, as it may become increasingly difficult to do so if the situation deteriorates further," an advisory on the Foreign Affairs website says.
"The Juba (South Sudan capital) airport is open, and tickets for commercial flights are available."
Federal government sources say about 100 Canadians are registered with the government as being in the African country.
South Sudan officials blame ethnic tensions for the violence that started last weekend and world leaders are concerned it could ignite a full-blown civil war.
The south fought a decades-long war with Sudan before a 2005 peace deal resulted in a 2011 referendum that saw South Sudan break away from the north, taking most of the region's oil wealth with it.
On Saturday gunfire hit three U.S. military aircraft trying to get American citizens out of a remote region of South Sudan.
The region has become a battle ground between the country's military and renegade troops, officials said.
The U.N. Security Council on Friday said the week long violence could affect neighbouring countries and the entire region.
Rick Roth, a spokesman for Foreign Affairs Minister John Baird says Canada is deeply concerned about the violence.
"Canada calls for an immediate stop to the fighting in South Sudan and expresses its strong support for the efforts of the UN mission and the African Union to help the parties resolve the current conflict through dialogue," Roth said in an email.
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