One U.N. officer was wounded during the meeting at Unity state, which was attended by several staff members of the world body, according to Kouider Zerrouk, a spokesman for the U.N. mission in Juba.
Seven U.N. staff members and three local officials traveled to Mayendit County to investigate a wave of violence from cattle raiding on the borders of Unity and Warrap states.
During the meeting Wednesday, the county commissioner from neighboring Lake state appeared and interrupted the meeting, yelling angry remarks at his Mayendit county counterpart, the spokesman said.
The shooting followed soon after.
"Four pick-up trucks carrying armed men believed to be the SPLA (South Sudan army) and SSPS (South Sudan police service) then appeared and started shooting indiscriminately at the Mayendit county commissioner's compound," Zerrouk said.
A local official said it was unclear why the Lake state official had an armed convoy.
"We are asking ourselves why the county commissioner would come with such a heavily armed convoy," said Gideon Gatpan Thor, the minister of information for Unity state. "He was uninvited, so we are still asking him to answer these questions. We want to know what his intentions were."
The clashes killed at least 16 people from Unity and 21 from Lake, including six civilians from both states, the minister of information said.
The U.N. officer injured in the attack is in stable condition at a hospital in Juba, South Sudan's capital.
"It appears that the U.N. team was not the target of the attack but were at the wrong place at the wrong time and were caught up in the incident," the minister of information said.
The meeting was initiated after a violent cattle raid four days earlier in Warrap state. The attackers, believed to be from Unity state, stole thousands of cattle and killed 74 people. Most were women and children.
The latest clashes come after a particularly violent month of cattle raids in Jonglei state. In late December, officials in the town of Pibor said more than 3,000 were killed in cattle raids after 6,000 armed youths from the Lou Nuer tribe attacked the Murle people.
The U.N. said the number is more likely in the hundreds, but it said 120,000 were affected and in need of immediate assistance.
Weeks later, the Murle attacked the Lou Nuer people in retaliation and killed more than 100 people in two separate attacks.
The main purpose behind the raids is to steal cattle, a livelihood for the people who live in the barren regions, but the violent clashes end with killings and child abductions.
The victims are largely defenseless women and children.
In a country struggling with violence six months into its independence, and recovering from decades of civil war, weapons have flown freely into the hands of cattle raiders.
What used to be rural-style attacks, with sticks and arrows, have been replaced by automatic weapons, killing thousands and displacing even more.
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