Australian soldiers are working in South Sudan's most troubled province of Jonglei, amid fierce fighting and allegations of ethnic cleansing, as the world's newest country collapses back into civil war.

Australian Colonel Mike Chadwick, the United Nation's senior military liaison officer in Jonglei, said the UN was managing under difficult circumstances.

More than 1000 people have died in the fighting in December. Foreign Minister Julie Bishop has urged all Australians to leave South Sudan immediately. Acting Prime Minister Warren Truss will brief the media about Australia's response to the conflict in Melbourne on Thursday.

Colonel Chadwick is one of 20 Australian Defence Force personnel, forming Operation Aslan, the Australian contingent contributing to the United Nations mission in South Sudan.

This week Jonglei became the front line in fighting between political and military rivals who represent two dominant tribes, the Nuer and Dinka.

"We are making a modest contribution," Colonel Chadwick said.

"But when the going gets tough and we are trying to work through an issue, time compressed and when the stakes are high, there is generally an Australian in every place that we link up to make it work."