More than 6,000 people have fled from southern South Sudan into the northern Ugandan district of Lamwo, recounting the slaughter of civilians by armed forces, according to the UN refugee agency.

A statement from the UNHCR said on Friday that more residents of Pajok town in South Sudan's Equatoria region were hiding in the bush trying to find their way to safety in Uganda.

"People fleeing the recent incident claimed that the town came under an indiscriminate attack by the South Sudan armed forces," the statement said.

The crisis comes after fighting between government forces and rebels erupted on Monday in Pajok in a previously peaceful part of the country that has seen a surge in conflict in recent months.

"Refugees told the UNHCR team on the ground in Lamwo terrifying stories of violence and abuse against civilians. Many have witnessed their loved ones shot dead or slaughtered like animals," Rocco Nuri, UNHCR spokesman, told AFP news agency.

"Families fled in all directions. Those unable to run were reportedly shot dead, including the elderly and people with disabilities."

A local pastor who fled Pajok on Wednesday, and asked not to be named, said soldiers had entered the town in tanks "and suddenly we saw shooting and we just had to run".

Both he and regional Anglican Bishop Oringa Benard reported that about 135 people had been killed; however, it could not be independently verified.

Uganda currently hosts more than 832,000 refugees from South Sudan, including more than 270,000 in the Bidibidi refugee camp, which in eight months has gone from an empty patch of land to the world's biggest refugee camp.

Government confirms

Michael Makuei, South Sudan government spokesman, confirmed its forces had attacked Pajok.

"As you know Pajok has been in the hands of the rebels so what happened was government forces went there and fighting ensued and so the civilian population that has been staying with the rebels had to run away," he said.

"I don't know the figure [of those who might have been killed or injured] but in any fighting there must be casualties."

READ MORE: Uganda at 'breaking point' from South Sudan refugee crisis

The UN peacekeeping mission UNMISS said in a statement on Wednesday it had twice been prevented from accessing Pajok.

"The mission has received reports of fighting between SPLA [government] troops and the opposition there and is trying to follow up on reports of civilians killed in the area," it said.

UNMISS urged the government to immediately allow it access "so it can fully implement its mandate, including to protect civilians and report on human rights violations".