The incident which occurred yesterday left more than 17 civilians dead.
An unknown number of fleeing civilians are said to have drowned in the Nile River.
More than 5,000 civilians had fled to the site last month, following deadly fighting between rival armed groups in Tonga, further west of Malakal.
The latest attack has also triggered violent inter-communal clashes among some internally displaced persons within the UNMISS protection of civilians (POC) site, according to a statement from the UN mission.
The mission said it sent peacekeepers to restore order and provide robust security on site.
“UNMISS calls on the attackers to cease hostilities immediately and refrain from harming vulnerable civilians and internally displaced persons,” it said.
The Mission is also calling on the state and national authorities to intervene urgently to de-escalate the situation and protect civilian lives.
“UN peacekeepers have been deployed to rescue drowning civilians and provide protection for the affected population.”
“The Mission is engaging all stakeholders concerned, including feuding parties, authorities, and local communities to enable a timely and collective response,” it said.