South Sudanese soldiers have looted UN stores and charities in troubled Jonglei state where the government has been battling rebels for a year, humanitarian sources told AFP on Sunday.

They said uniformed men ransacked and looted a hospital and premises of French aid agency Doctors Without Borders (MSF).

The men also "flattened" premises of the Italian aid agency INTERSOS and raided UN stores in Pibor town late on Saturday and Sunday, the sources said.

"The SPLA (army) went to INTERSOS and looted things there and then went to the World Food Programme and looted," Beko Konyi, coordinator for the state-run Relief and Rehabilitation Commission in Pibor county, said.

An MSF source said its hospital in Pibor was also ransacked.

"All the items from MSF are looted, everything, drugs and all the assets, and again INTERSOS," an eyewitness working for an international agency in Pibor told AFP.

Asking for anonymity for fear of reprisal, the eyewitness said the perpetrators were "SPLA", referring to the Sudan People's Liberation Army, or government forces.

"I'm here, I saw it with my own eyes," the eyewitness said.

Other sources told AFP that many South Sudanese soldiers were seen hauling away building materials, furniture and tents from aid agency compounds.

"MSF is deeply concerned about reports we are receiving that our health centre in Pibor town has been looted today", Sunday, said the group's head of mission in South Sudan, Vikki Stienen.

"We suspended medical activities in Pibor town on April 19 as the security situation had made it impossible to provide impartial medical care there."

He said that before the suspension, the population of Pibor and the surrounding area relied almost entirely on MSF for medical services.

"We know that the consequences for the population of the loss of access to healthcare are devastating," Stienen added.

Other international aid workers pulled out of Pibor on Friday over concerns about a possible rebel attack and rains cutting them off.

South Sudan's military spokesman Philip Aguer said he was unaware of the looting incidents but challenged the reports.

"Why would they go and do that? I doubt these are SPLA soldiers. These may be rebels," he said.

South Sudan has been fighting former soldier and theologian turned rebel leader David Yau Yau since April 2011.

An international aid worker in Jonglei insisted the looters were soldiers.

"It's absolutely SPLA, it's absolutely not rebels, if it is they are looting places 100 metres (yards) away from the army's barracks," the worker said, also speaking on condition of anonymity.