The northern army has been fighting southern troops it says are rebels for longer than a week, using bombs and jets.
Yesterday morning the north's Sudanese Armed Forces (SAF) jet fighters dropped 11 bombs in Kadugli and Kauda, aiming for an airfield, the UN said.
Planes carrying aid have been stopped from landing in the state capital Kadugli and roadblocks manned by armed troops have stopped aid workers getting through on land.
"This bombing campaign is causing huge suffering to civilian populations and endangering humanitarian assistance,” said the UN’s spokesman Kouider Zerrouk.
He called on the SAF, SPLA (Sudan People's Liberation Army) and other armed groups who are involved in the fighting to let through aid workers and stop indiscriminate military attacks on ordinary people.
The United Nations High Commissioner for Refugees said the lack of security has severely hampered aid work and the agency can’t get to a warehouse only two miles from the UN peacekeeping base.
And the World Food Program and the World Health Organisation said buildings belonging to the two UN agencies in the area had been looted.
The fighting comes at a tense time for the north east African country, with the south fixed to declare independence from the north in less than a month. But there is still no consensus on several aspects of the split including where the border should be drawn and how to share oil money.
Southerners voted to become independent in a January referendum which was promised in a 2005 peace deal that ended decades of north-south civil war which killed two million people.
The UN refugee agency said it knew there were at least 41,000 people in the state who have been forced to flee their homes. The agency also fears that many more are leaving, mostly children and women. And when some of the fleeing children and old people can’t keep up with the rest of the family, they get left behind.
Aid agencies have only been able to get food and help to 6,000 people, it said. "This is far below the number we would be able to reach if we had secure access," said a spokeswoman.
Southern Sudan's leader, Silva Kiir, has said he will not return to a war that could jeopardize the south's independence.