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At least 16 civilians were killed in fighting on Monday between government troops and rebels in South Sudan's second-largest city Wau, the United Nations peacekeeping mission (UNMISS) said in a statement.

The violence stemmed from an ambush of government troops near the city on Sunday, leading to clashes the following day, UNMISS said.

"The Mission mounted two patrols into Wau on Monday and said it had observed the bodies of 16 civilians in a hospital. There were ten people who had been injured," the statement said.

Wau is located in a region that has repeatedly changed hands between government troops and rebels loyal to former vice president Riek Machar since the country descended into civil war in 2013.

The city itself has remained under the control of forces loyal to Machar's arch-enemy President Salva Kiir throughout.

UNMISS said troops, tanks and equipment from the SPLA national army had moved towards areas controlled by the rebels in the south-western part of Wau late last week.

At least 3,000 people, mostly women and children, sought shelter in a Catholic church, while another 84 had sought refuge at an UNMISS Protection of Civilians site.

The International Committee for the Red Cross said it was rushing surgical teams to the city to assist the wounded.

The military and rebels gave conflicting accounts of the violence.

Military spokesman Colonel Santo Domic Chol said the fighting started as government troops were trying to rout rebels from strongholds in the countryside.

South Sudan's leaders fought for decades for independence, but once they got it in 2011, civil war erupted in 2013 out of a power struggle between Kiir and his former deputy Machar.

At least 1.7 million people have fled the country because of the war, and 1.9 million are internally displaced.

The war has also created a man-made famine, exacerbating a dire humanitarian crisis.