The UN has sent reinforcements to the base at Akobo in Jonglei state and to help other groups fearing for their lives amid a worsening showdown between President Salva Kiir and his former vice president, a spokesman said.
Ethnic Nuer youths forced their way into the small UN mission in Akobo where more than 30 ethnic Dinka had sought shelter, UN deputy spokesman Farhan Haq said.
"Fighting took place," he told reporters. "We fear there may have been some fatalities but can't confirm who and how many."
The attack was the latest reported as fighting spreads across South Sudan between army factions split between Salva Kiir, an ethnic Dinka, and former vice president Riek Machar, a Nuer.
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UN forces are also protecting 14,000 civilians gathered around a base in Bor, capital of Jonglei state, and protecting the Bor airstrip, Haq said.
Hundreds have been killed in the capital, Juba, alone since clashes between rival factions of the Sudan Sudanese army erupted on Sunday.
Haq said there were unconfirmed reports of several students killed by security forces at Juba University yesterday.
Between 2,000 and 5,000 civilians have gathered in another part of Juba, the Kator complex, and had also requested help from UN Mission in South Sudan (UNMISS) peacekeepers, Haq said.
More than 15,000 people have sought shelter at two UN and one World Food Programme compounds in Juba.
Haq said that food and water supplies and sanitation at the compounds are "overstrained".
"Violence is spreading and could spread even further and we need all South Sudanese leaders and political personalities now to immediately appeal to calm and call on their supporters to suspend hostilities," said UN deputy secretary general Jan Eliasson.