Global aid organisation Oxfam has withdrawn 22 staff from South Sudan's Upper Nile state because of escalating violence along the newly independent country's tense border with the north.

Relations between the two countries have deteriorated sharply over the past week, due to fighting either side of the new frontier, including alleged cross-border attacks by the Sudanese army that Khartoum has strongly denied.

Oxfam staff reported bombing and heavy artillery for several hours on Friday in Upper Nile state, as well as planes flying overhead and a build-up of South Sudanese troops, in a statement released late on Saturday.

The aid agency said 50,000 people have fled across the border from Sudan's war-torn Blue Nile state since the fighting erupted there in early September between the army and southern-aligned rebels, and that thousands of refugees continue to arrive.

"New bombing raids and a build-up of troops along the border of Sudan and South Sudan over the past few days threaten to escalate what is already a significant humanitarian crisis in the newest country in the world," it said.

Oxfam's 22 staff members being relocated were mainly engineers and health workers working in the Upper Nile towns of Jamam and Renk, near the border.

On Thursday, southern officials accused the Sudanese army of bombing a refugee camp in nearby Unity state, very close to the northern state of South Kordofan, sparking international outcry.

Analysts warn that, while the prospect of a full-scale conflict between the former civil war enemies is still remote, cross-border skirmishes are likely to continue, creating a state of permanent antagonism and undermining negotiations on post-secession issues.