More than 40 people died in days of fighting in a South Sudan town, the government said Tuesday, with aid agencies warning of dire conditions for over 10,000 people sheltering at a UN base.

At least 39 civilians and four policemen were killed in the town of Wau, some 650 kilometres (400 miles) northwest of Juba, since violence broke out on June 24, Minister of Information Michael Makuei told reporters.

The town was reportedly calm on Tuesday after days of violence, which the army spokesman said was caused by "anti-peace elements supported by tribal fighters".

"These are the bodies that have been found so far but the cleaning continues," Makuei said. "Probably the number may rise."

Civil war erupted in South Sudan in December 2013 but rebel chief Riek Machar returned to the capital in April as part of a peace deal which saw him become vice-president, forging a unity government with President Salva Kiir.

But fighting continues between multiple militia forces who now pay no heed to either Kiir or Machar.

READ: Aid workers hit by increased South Sudan violence

Peacekeepers from the UN mission (UNMISS) opened the gates to their base in Wau to shelter over 10,000 civilians, cramped inside the protection of the razor wire fence.

"Water and sanitation conditions at the crowded UNMISS base are critical," the International Organisation for Migration (IOM) said Tuesday.

More than 160,000 civilians are now in UN-guarded camps across the country, down from a peak of more than 200,000 at the height of the war.

Tens of thousands have died in the conflict, forcing two million from their homes and leaving five million in need of help.

Festus Mogae, a former Botswana president who heads the international ceasefire monitoring team, said last week that progress "expected has not materialised" and that "if anything, the parties are further apart."