UN troops in the flashpoint Abyei region shot and killed one of the mission's own employees who had joined a tribal dispute, an Abyei resident familiar with the situation said on Wednesday.

UN officials confirmed that a member of the Dinka tribe who worked for the UN's Interim Security Force for Abyei (UNISFA) died after clashes with the peacekeepers.

The incident is the most serious in the region since Sudanese troops withdrew in May to end a year-long occupation that forced more than 100,000 people to flee Abyei towards South Sudan.

It adds to tensions before an early-December deadline for Khartoum and Juba to settle the final status of Abyei, the most sensitive matter left unresolved when the South separated last year.

The dead man was among a group of Dinka youths who harassed leaders of the nomadic Arab Misseriya tribe who went to Abyei town to meet the UNISFA commander, the Abyei resident said.

Because the town is still deserted and devoid of facilities, the group of about 20 Misseriya had spent the night at the local mosque, which the Dinka began stoning around dawn on Tuesday, said the resident, who asked for anonymity.

"A group of Ethiopian military was pushing these people, trying to stop them from stoning," but the peacekeepers were also targeted by the rocks, leaving one injured, the resident said.

Two of the Dinka then directly confronted the troops, trying to seize their weapons, the source added.

Peacekeepers fired warning shots into the air but one man who continued trying to seize a weapon was shot and killed. He worked in administration for UNISFA, the source said, adding that a UNISFA labourer was shot and wounded.

Dinka are a dominant tribe in South Sudan.

Damian Rance, a public information officer with the UN's humanitarian agency in Khartoum, confirmed that a Dinka UNISFA employee "was shot and killed".

In New York, the spokesman for UN chief Ban Ki-moon said late Tuesday that "one national staff member succumbed to his injuries and another sustained an injury as a result of clashes in Abyei between UNISFA and Ngok Dinka demonstrators.

"UNISFA has established checkpoints and is monitoring movements into Abyei. UNISFA's leadership is also meeting with Dinka and Misseriya representatives in an effort to defuse tensions," he said.

Rance said he understood that tensions rose on Monday when Misseriya tribal chiefs went to Abyei town for a meeting with the head of UNISFA, upsetting the Dinka.

"UNISFA put up security and the crowd dispersed," Rance said.

The deadly clash occurred the following day.

"Now the situation is under control," the Abyei resident said.

Early Wednesday UN chief Ban condemned "the series of incidents that occurred in Abyei in the past 48 hours" and urged the communities to resolve their disputes through dialogue.

Ban said he remained extremely concerned that joint institutions, including police for the Abyei area, have not yet been established.

Sudan and South Sudan in late September signed agreements on oil and border security which they hailed as ending their conflict after a war along their undemarcated frontier in March and April.

Despite those pacts reached through African Union mediation, they could not finalise the status of Abyei and other disputed border areas.

Abyei was to hold a referendum in January 2011 on whether it belonged with the north or South, but disagreement on who could vote stalled the ballot.

The AU set a December 5 deadline for the two countries to resolve Abyei's final status or be bound by an AU proposal for a referendum in October next year.

Under that proposal, Dinka would have the right to vote, along with Sudanese with "permanent abode" in the Abyei area.

Sudan's President Omar al-Bashir vowed last week that "all Misseriya will participate in the Abyei referendum."