A spokesman for the rebels said the violation indicated "the lack of seriousness" the government of President Salva Kiir Mayardit had for the agreement, the Sudan Tribune reported.
South Sudanese troops had attacked rebel positions in Unity and Upper Nile states within the last few hours, said James Gatdet Dak, a spokesman for the forces of ousted vice president Riek Machar.
Dak said government forces had moved out of Bentiu, the capital of Unity, and attacked rebel forces about 30 miles to the south.
He claimed pro-government forces attacked rebel-held areas in Upper Nile state.
"This clearly indicates the lack of seriousness on the part of the government to respect the agreement," he said.
The alleged violation came as the U.N. World Food Program announced it would take advantage of the break in conflict to to deliver food aid to areas of South Sudan that had been difficult to reach. WFP is already distributing food to more than 200,000 people in refugee camps in Upper Nile and Unity states.
In a statement, WFP country director Chris Nikoi said it is "important to note that humanitarian needs will continue, long after the fighting stops."
The two sides reached a cessation of hostilities agreement Thursday after negotiations mediated by the Intergovernmental Authority on Development.
Clashes between government forces and rebel groups broke out Dec. 15 after Machar allegedly attempted to stage a coup. Machar, who was pushed out of office when Kiir reshuffled his Cabinet in July, denied attempting a coup.
As part of the agreement, both sides must "refrain from taking any actions that could lead to military confrontations, including all movement of forces, ammunition resupply or any other action that could be viewed as confrontational."
Both leaders said Thursday's cease-fire was a temporary measure and negotiations would have to continue to reach a formal peace agreement, the New York Times reported Friday.