The UN has accused the Sudanese government of carrying out an "intensive bombing campaign" near the north-south border.
This has led to "huge suffering" for civilians in South Kordofan, it says.
Northern forces are accused of targeting the area's pro-southern groups, as oil-rich South Sudan prepares for independence next month.
The bombing follows a deal for both sides to withdraw from the nearby disputed town of Abyei.
Clashes over the past month in Abyei and South Kordofan have raised fears of renewed north-south conflict despite a 2005 peace deal which paved the way for the end of decades of war.
Some 140,000 people have fled the fighting.
Although South Kordofan is north of what will soon be the international border, it is home to many pro-south communities, especially in the Nuba Mountains, some of whom fought with southern rebels during the long civil war.
"We are extremely concerned about the bombing campaign, which is causing huge suffering to the civilian population and endangering humanitarian assistance," Kouider Zerrouk, spokesman for the UN mission in Sudan, told AFP news agency.
He said two of the bombs had landed near the UN base in Kauda, close to an airstrip that was apparently being targeted. Mr Zerrouk said the bombing started a week ago.
Aid agencies looted
In addition, aid workers say, ethnic Nubans are being targeted by the northern military and Arab militias.
"People are being hunted down for their ethnicity," John Ashworth, an adviser with the Sudan Ecumenical Forum, told the BBC's Focus on Africa programme.
He said many areas inhabited by ethnic Nubans were being bombed and shelled and that people had fled further into the area's hills and mountains to escape the attacks.
But this was denied by Rabbie Abdelattif Ebaid, an adviser to Sudan's information minister, who said rebel fighters were being targeted.
Some 40,000 people are estimated to have fled their homes in South Kordofan, on top of some 100,000 in Abyei, which was seized by northern forces last month.
Amnesty International's Tawanda Hondora said he suspected a well-planned campaign was being implemented, to rid South Kordofan, Unity State and Abyei of "people who are perceived to be sympathetic to the south."
Aid agency offices have been looted, churches have been ransacked and buildings destroyed.
Talks between Sudanese government officials and representatives of the south are continuing following Monday's deal for both sides to withdraw from Abyei.
President Omar al-Bashir and southern leader Salva Kiir agreed that Abyei, claimed by both sides, would be demilitarised with Ethiopian troops ensuring security.
However, no time frame has been published.
Ahead of the south's independence, the BBC's Peter Martell in South Sudan says several issues have yet to be resolved:
- How to share Sudan's oil wealth - it is currently 50-50
- The demarcation of the border
- Citizenship criteria for the two countries
The north-south war ended with a 2005 peace deal, under which the mainly Christian and animist south held a referendum in January on whether to secede from the largely Arabic-speaking, Muslim north.
Some 99% of voters opted for independence. President Bashir said he would accept the verdict of the south, where most of Sudan's oil fields lie.