According to Aguer, forces loyal to former vice president Riek Machar have taken control of the city after the Sudan People's Liberation Army troops withdrew, "but the fighting is still going on", Xinhua reported.
Aguer further explained that the forces, which attacked Bor were a mix of defected soldiers, rebels following commander Peter Gadet and a militia known as "White Army" comprising fighters from the Nuer tribe to which Machar belongs.
"Machar is trying, by all means, to seize power by force, and to do so he uses the forces of Nuer tribe and all the rebel groups against the state," Aguer added.
Machar announced on Tuesday his agreement on an immediate cease-fire and negotiations with the government, but Aguer said at the time of the announcement, "his forces were attacking Bor".
During the past two weeks, South Sudan has witnessed clashes between two military factions, one descending from the Dinka tribe, to which South Sudanese President Salva Kiir Mayardit belongs, and the other descending from the Nuer tribe, to which Machar belongs, who is accused of plotting to topple the government.
According to UN reports, the clashes have left thousands dead and 121,600 civilians displaced. About 63,000 people have taken refuge at various UN compounds across the country.