0822 GMT June 22, 2018
The IOM said on Thursday the convoy was attacked two days ago while returning from the central town of Yirol where staff and health workers were assisting communities affected by a deadly cholera outbreak.
An IOM health officer is among the injured, the organization said in a statement. It was not immediately clear who the other victims were.
IOM Director General William Lacy Swing condemned the attack as "appalling", saying it came during a lifesaving humanitarian mission.
"In a country overwhelmed by the huge lack of basic necessities due to conflict, famine and health epidemics, these types of attacks undoubtedly harm the ability of humanitarian partners to provide assistance to millions in need of lifesaving aid," Swing said.
Some 100,000 people are suffering from a man-made famine in South Sudan.
Another one million people could be hit by famine if there is insufficient rain in the coming months and a total of nearly five million will be going hungry.
Drought has forced many to drink from unreliable water sources, resulting in diseases such as cholera which has affected 300 people and left 10 dead in Yirol.
The three-year civil war in South Sudan has made it difficult for aid workers to reach affected areas.