The warring sides traded blame for breaching the terms of a peace deal, brokered by the regional eight-nation IGAD bloc along with the United Nations, the African Union, China, Britain, Norway and the United States.
"Riek Machar's rebels attacked Malakal yesterday (Friday)", and the "assault on Malakal resumed this (Saturday) morning," army spokesman Colonel Philip Aguer told a press conference.
"We want the IGAD to establish the presence of a ceasefire mechanism in all the counties," Aguer said.
"They wanted to seize the area before the ceasefire comes into effect," he said.
Also Read
It was not immediately clear if the ceasefire had entered into force today afternoon in the world's newest nation which broke away from Sudan four years ago. Dak said it was supposed to come into effect at midnight.
Information minister and government spokesman Michael Makuei said: "This is of course a violation of the cessation of hostilities of the agreement and it should be recorded."
"We suspect that their plan is to launch a full-scale offensive against our bases around Malakal. This is a serious violation of the terms of the peace agreement," a rebel statement said.
But IGAD spokesman Hailemichael Gebreselassie disclaimed any knowledge of the clashes, saying: "We haven't heard anything related to any incidents."
The accord, signed by rebel leader Machar on August 17 and the government only on Wednesday, gave a 72-hour deadline for a permanent cessation of hostilities.
Aguer said the rebels attacked Malakal, the state capital of Upper Nile, overnight "using mortars and machineguns" and resumed shelling today.