The UN has received reports of some casualties, it said.
"At the time, 43 Indian peacekeepers, six UN police advisers and two civilians of the UN were present at the base. About 30 South Sudanese had sought shelter from the turmoil plaguing areas of Akobo County," a statement issued by United Nations Mission in South Sudan (UNMISS) said.
The UNMISS strongly condemned the attack on its base in the Jonglei State town of Akobo by unknown assailants.
The mission said it is doing everything possible to ascertain the circumstances surrounding the assault on the base and secure the safety of its personnel who remain there.
"The Mission will dispatch its aircraft early today morning to evacuate UN personnel. The Mission fully expects all forces, whatever their allegiance, to ensure the safety of UNMISS personnel and any civilians located inside Mission premises," it said.