The ceasefire, aimed at stopping five weeks of bitter fighting in which thousands have died, began Friday evening with both sides reporting clashes as the deadline approached.
But Ateny Wek Ateny, spokesman of President Salva Kiir, insisted they would honour the agreement.
"We are definitely going to maintain a ceasefire," Wek said, adding that government forces had responded only in self-defence to rebel attacks. "All we hope is that both sides respect the peace deal."
The fighting has been marked by atrocities on both sides with some 700,000 people forced from their homes in the impoverished nation, according to the United Nations.
Today morning, in the first hours of the ceasefire, army spokesman Philip Aguer said the clashes appeared to have ended.
But just hours later, the government reported fresh rebel attacks.
"Rebel forces are still continuing attacking our forces," Minister of Information Michael Makuei said, speaking to reporters as he arrived back from the talks in Ethiopia that hammered out the crucial deal. "Our forces... Will have to defend themselves," he added.
"This is not strange, these are rebels and... Rebels are indisciplined people, they have no regular forces, no central command," Makuei said, although he added that the weeks of negotiation efforts in a luxury hotel in Addis Ababa were not "wasted time".
He did not give any details of the scale of the latest fighting, or where the reported clashes had taken place.
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