The South Sudanese Community Association has said it is regretful that South Sudanese Australians had chosen to engage in the conflict in South Sudan.
SBS has revealed up to 30 South Sudanese Australians have travelled back to their homeland to join the conflict.
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They have taken up with both of the warring parties, with some loyal to the government forces controlled by President Salva Kiir and others siding with opposition leader Riek Machar.
The Australian government and opposition are yet to respond to SBS requests for comment on the issue.
The chairman of the South Sudanese Community Association, Kot Monoah said choosing to participate in a foreign war is an individual choice and not a community choice.
"Choosing to fight a war for, or against, the government is not acceptable."
But he said ultimately, an individual must account for his actions.
"They must not fight wars overseas and choosing to do so comes with accountabilities," Mr Kot said.
"Choosing to fight a war for, or against, the government is not acceptable."
Mr Kot said he encouraged all South Sudanese Australians to take the opportunities available to them in Australia and to be better citizens here.
"We migrated to Australia some years ago looking for better lives and a place save (sic) and free of wars," he said. "We must live the dreams that make us migrate in the very first place."
Mr Kot also urged South Sudanese Australians involved in "hate comments based on ethnic basis" to stop.
"It is regretful that many do not understand that they will one day account for their cyber role in fuelling conflict in South Sudan," he said.
International law Professor, Ben Saul, said it was potentially lawful for a dual Australian-South Sudanese citizen to fight for national armed forces.
But he said any Australian citizens involved in fighting for a non-state armed group, could face heavy penalties under Australia's Foreign Incursion and Recruitment offences.
