World Food Programme says contract workers were hacked to death with machetes and shot in violence earlier this week.
The World Food Programme said on Friday it was "horrified" to learn that three of its South Sudanese workers were killed in violence that claimed at least 16 lives earlier this week.
The three men, contracted as porters, appear to have been killed while trying to get to a WFP warehouse amid fighting between rebel and government troops near the western city of Wau.
Two were hacked to death with machetes and one was shot dead, the UN agency said.
South Sudan, which split from Sudan in 2011, has been mired in a crisis since a power struggle between President Salva Kiir and his former deputy Riek Machar escalated into a military conflict in 2013.
Joyce Luma, the WFP country director, said: "We are outraged and heartbroken by the deaths of our colleagues, who worked every day to help provide life-saving food to millions of their fellow countrymen."
She called on South Sudanese authorities to hold the attackers accountable.
Prior to the killings of the WFP staff, the United Nations said at least 79 of its aid workers have been killed since December 2013.
Attacks on aid workers and obstruction of their work have contributed to a man-made famine affecting 100,000 people and threatening another one million in the country.
Last month, three Kenyans and three South Sudanese aid workers were hauled from their vehicle and shot dead in an ambush - the deadliest single attack on aid workers since the war began.
Some 8,000 people have fled the clashes in Wau, the International Organisation for Migration said on Thursday. They join more than 3.5 million South Sudanese displaced by the war.
Witnesses told news agencies that government-aligned militia had targeted residents based on their ethnic group who are seen supporting the rebels.
"The pattern of abuses by government forces against civilians in Wau has become predictable, with soldiers taking revenge against unarmed civilians based on their ethnicity," said Human Rights Watch’s Daniel Bekele in a statement.
The UN said in December it had evidence of ethnic cleansing by both government forces and rebels.