The assessment by Haile Menkerios to the UN Security Council came as the peacekeeping mission welcomed an agreement between the rival sides to bolster security after deadly fighting in and around the flashpoint district.
The UN Security Council powers all praised the referendum in south Sudan which is expected to lead to the breakup of Africa's biggest nation.
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But all expressed concern about tensions in Abyei where dozens died in clashes last week and the United Nations has sent peacekeeper reinforcements to prevent new fighting.
Uncertainty over region's future
Menkerios said that uncertainty over the future of Abyei, which had been due to hold a simultaneous plebiscite alongside the wider southern referendum that has been indefinitely postponed, meant there was "a risk of instability" for months to come.
More than three days of fighting this month between migratory Misseriya Arab nomads from the north and settled pro-southern Dinka Ngok killed between 20 and 60 people, Menkerios told the Security Council.
There have also been a series of ambushes against buses carrying southerners home from the north for the independence vote that have claimed at least 10 lives.
The attacks prompted authorities in the south to suspend returnee convoys through the area, UN Sudan humanitarian coordinator Georg Charpentier told reporters in southern capital Juba on Saturday.
Talks in the north Sudanese town of Kadugli on Monday between the Sudanese interior minister and southern internal affairs minister and leaders of the rival groups resulted in agreement on new measures to reduce tensions, the UN mission said.
Joint patrols to step up
Patrols by special joint units of northern and southern troops, which are the only armed groups other than UN peacekeepers allowed to enter Abyei, are to be stepped up.
"The key measures of this agreement include... the provision of security for Abyei by deploying more Joint Integrated Units, ensuring the freedom of migration for Misseriya nomads to Abyei and southwards; and providing security for the movement of internally displaced persons (IDPs) returning home," said a UN Mission in Sudan (UNMIS) statement released Tuesday.
"The agreement builds upon and widens the accord between the Misseriya and the Dinka Ngok reached last week in Abyei," it added.
Under the agreement reached on Thursday, two battalions of UN troops were sent to northern Abyei and 300 Dinka Ngok police were withdrawn, Menkerios said.
UNMIS "has increased both the size of it military deployment to Abyei and its military-civilian patrolling in the area in order to deter further clashes," Menkerios said.
But he added that there had been attempts to commandeer UN vehicles and "direct threats" to UN personnel.
"These efforts for reducing tensions and preventing violence can contain the situation. However, the continued absence of a final settlement on the future of Abyei leaves open the possibility of further clashes between the communities," he told the council.
Deadlock between north and south over who should be eligible to vote in Abyei forced the postponement of the planned plebiscite on its future. The Misseriya nomads insist they should have the same rights as the settled Dinka.
Menkerios said the south Sudan referendum was still an "historic milestone" in the implementation of the 2005 peace accord which ended a 22-year civil war between north and south that claimed an estimated two million lives.
