The truce brokered by the regional eight-nation IGAD bloc, along with the United Nations, African Union, China, Britain, Norway and the United States, came into effect last evening at 2100 GMT (midnight in South Sudan's capital Juba).
But it was unclear whether it would hold.
Earlier yesterday, South Sudan's army and rebels accused each other of sparking fresh fighting in the past 24 hours in the north-east.
Aguer said the rebels used mortars and machineguns and that one government soldier was wounded.
The "assault on Malakal resumed Saturday morning," he said, insisting the army had a right to respond in self-defence.
Rebel spokesman James Gatdet Dak denied his camp had fired first.
"That's untrue, their forces attacked us near Malakal," he said.
"They wanted to seize the area before the ceasefire comes into effect," he added.
A peace deal signed by rebel leader Machar on August 17, but only signed by President Salva Kiir on Wednesday, gave a 72-hour deadline for a permanent cessation of 20 months of hostilities.
Aguer, the army spokesman, called on IGAD to establish a ceasefire monitoring mechanism "in all the counties".
But IGAD spokesman Hailemichael Gebreselassie denied any knowledge of the latest clashes, saying: "We haven't heard anything related to any incidents.
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