"We recaptured Bor yesterday evening, just before sunset, and this morning there are currently operations against some pockets of rebels within the airport area," Information Minister Michael Makwei told AFP.
"The army is clearing them up... But most of the rebels who were in the town are on the run," he said, adding that Defence Minister Kuol Manyang had already returned to Bor, his hometown, to lead the operation.
"There is fighting now in Malakal since morning between the government forces and the rebels," Makuei added. "It is not true that the rebels have taken over."
Bor's capture, apparently without major resistance by the rebels, lifted nearly a week-long seige of the town, where some 17,000 civilians fled into the overstretched United Nations peacekeeping compound for protection, severely stretching limited food and supplies.
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While its recapture is a significant victory for the government, rebel forces still control vast swathes of Jonglei state, and still hold the town of Bentiu, capital of crucial oil-producing Unity state.
Fighting has gripped South Sudan for more than a week, after President Salva Kiir accused his former deputy Riek Machar, who was fired from the government in July, of attempting a coup.
The UN humanitarian chief in the country, Toby Lanzer, said yesterday that there was "absolutely no doubt in my mind that we're into the thousands" of dead, the first clear indication of the scale of the conflict engulfing the country.
Vowing to oust Kiir, his forces seized the town of Bor, located just 200 kilometres north of Juba, late today.