The United Nations is scrambling emergency aid to more than 40,000 people displaced by floods in southern Sudan, a top regional official said on Thursday.

Seasonal heavy rains in Northern Bahr el-Ghazal state caused the Kuom river to overflow in the town of Aweil, making 39,000 people homeless in the region, officials said.

"This is an area of concern for us and we are looking to getting people on the ground quickly," UN regional coordinator for southern Sudan, David Gressly, told journalists.

Floods have displaced a further 1,500 people in 14 villages of neighbouring Warrab state, Gressly added.

Conditions in the annual floods have not reached levels of previous years.

"The UN is working quite closely with the government of Northern Bar el-Ghazal, which has set up a crisis management committee," Gressly said.

"Assessments are underway, as well as an initial response to supply food, non-food items, kitchen sets, sleeping mats (and) mosquito nets to help support those displaced by the floods."

The high water levels have raised fears of increased cases of cholera, typhoid and malaria.

Rain has also hampered efforts to support some 50,000 people who fled south from fighting last May between northern and southern forces in the contested oil district of Abyei.

"Conditions continue to deteriorate because of the rains," Gressly said.

The Abyei violence was seen as the biggest threat to the Comprehensive Peace Agreement that ended 21 years of civil war between north and south Sudan in 2005.

The town of Abyei was left in ruins after the fighting.

"Until the situation in Abyei is resolved with a full withdrawal of all forces, the establishment of a joint police force, an integrated unit on the military side and an interim administration, it is unlikely that there will be a major movement of people back," Gressly added.