“We have enough forces who will defeat the rebels within 24 hours,” army spokesman Philip Aguer told reporters.
“These forces – the rebels – are now retreating back.”
Almost three weeks of violence in South Sudan has forced around 200,000 people to flee their homes and affected many hundreds of thousands of people indirectly, the UN has warned.
Thousands of people are feared to have been killed in the fighting, pitting army units loyal to President Salva Kiir against a loose alliance of ethnic militia forces and mutinous army commanders nominally headed by ex-vice president Riek Machar.
Bor, the capital of Jonglei state and situated just 200 kilometres (125 miles) north of the capital Juba, One of the hardest hit areas.
It has changed hands three times since the fighting erupted, forcing thousands to seek shelter in badly overstretched United Nations peacekeeping bases, and tens of thousands to flee across the crocodile-infested White Nile river.
The rebels retook the town on Tuesday, but on Thursday, the army said they were advancing again to push them back.
“I doubt if they can spend the night in Bor, and I am sure this evening they will move to the north of Bor,” Aguer added.
Meanwhile government and rebel negotiating teams are at a luxury hotel in neighbouring Ethiopia’s capital Addis Ababa, in the first stages of trying to hammer out a ceasefire deal.