Unknown assailants on Thursday attacked United Nations base in Bor town of Jonglei State.
The attack killed and injured civilians who went for protection during violent clashes between government forces and rebels.
The UN Secretary-General Ban Ki-moon said he was shocked to learn attack on UN Mission base in Akobo.
He urged government and opposition forces to respect the rights of civilians and ensure their safety and security.
The UN Chief said UNMISS was doing everything it could to protect civilians, UN and international personnel on the ground.
Mr Ki-moon said there were indications that civilians were killed and wounded in the attack.
He called for the verification of the report and those responsible held accountable for their crimes.
The number of people that fled to UN installations reached 35 thousand.