Aircraft dropped several bombs in two attacks targeting a transit centre in South Sudan with some 5,000 refugees, with one boy wounded and 14 others missing, the UN refugee agency said Tuesday.

"At least one Sudanese refugee boy is injured and 14 others missing following an air raid in South Sudan Monday," the UNHCR said in a statement.

"UNHCR is alarmed by this attack on vulnerable refugees already fleeing violence in Sudan's Blue Nile state."

The attack took place in South Sudan's Upper Nile state, less than 10 kilometres (six miles) from the border with Sudan, as UN staff tried to relocate refugees further inside South Sudan for safety.

"It was carried out in two instances with several bombs falling at the refugee transit site... about 5,000 refugees were at the site," UNHCR added. "Refugees jumped out of the trucks and scattered. Agency staff also had to seek safety."

South Sudan -- which declared independence from former civil war enemies in north Sudan in July -- has accused Khartoum of launching several bombing raids in frontier regions of its territory, claims denied by the northern army.

Fighting erupted in Sudan's Blue Nile state in September between government forces and gunmen formerly allied to the now independent South Sudanese army.

The fighting in Blue Nile followed an eruption of a conflict last June in Southern Kordofan state, where Khartoum is also battling Nuba rebel forces, who are also former southern allies.

Over 78,000 people have fled into the South Sudan from the north since August last year.

In addition, the South hosts over 110,000 people who fled last May from the contested border region of Abyei -- which both north and south claim as theirs.