South Sudan's rebel chief on Monday accused the government of breaking a ceasefire, jeopardising a peace agreement aimed to end the country's 20-month civil war.

"We have concerns that the ceasefire is not holding, and this is because the government is unable to control its own troops," Riek Machar told reporters in the Ethiopian capital.

There was no immediate response from South Sudan's army, but it called similar claims on Sunday a "fabrication".

The reports of clashes were not possible to verify independently.

Rebels said an army convoy of river barges had attacked their positions along the White Nile river.

"For the government, lauching this convoy on the Nile is a serious violation of the ceasefire," Machar said. "It provokes our troops that are in control of those areas."

President Salva Kiir on Wednesday signed a peace accord, already signed by Machar.

The ceasefire came into effect on Saturday evening, hours after fresh clashes between government forces and rebels.

Over two million people have fled their homes in a war marked by ethnic killings, gang rapes and the use of child soldiers. Some 200,000 civilians are sheltering inside UN bases.

Ceasefire monitors from the regional East Africa bloc IGAD, which led efforts to negotiate the peace deal, said their teams would investigate the claims.

"These are serious allegations that need verification," an IGAD spokesman said.

The civil war began in December 2013 when Kiir accused Machar, his former deputy, of planning a coup, setting off a cycle of retaliatory killings that has split the impoverished country along ethnic lines.

Faced with the threat of international sanctions, Kiir finally signed the peace deal but annexed a list of reservations that he said would have to be addressed for the deal to take hold.

"We question the political will of the government to implement the peace agreement," Machar added.

The UN Security Council has threatened sanctions against anyone who undermines the accord.