Malakal, the main town in northern Upper Nile state, has become one of the most bitter battlegrounds in the conflict now raging for over a month in the world's youngest nation.
On Monday, rebels staged an assault to seize back Malakal -- which has switched hands twice -- but both the government and rebels have insisted they are in control.
"The commander in Malakal has not been accessible since yesterday," army spokesman Philip Aguer said, without giving further details.
Dozens of civilians were wounded as stray bullets landed inside the UN base, with peacekeepers firing warning gunshots to keep warring sides away.
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Rebel spokesman Lul Ruai Kong, speaking in neighbouring Ethiopia, claimed earlier this week to have taken the town.
Telephone networks are apparently no longer working in the area, and South Sudan's Minister of Information Michael Makuei insisted late Thursday the town remained "fully under our control", and called rebel claims a lie.
Aguer said there had been no reports of fighting on Thursday there, but insisted the army is still "moving to Bor".
Up to 10,000 people are believed to have been killed so far in the fighting pitting forces loyal to President Salva Kiir against a loose coalition of army defectors and ethnic militia nominally headed by Riek Machar, a former vice president and seasoned guerrilla fighter.
The attack on Malakal came days after the government recaptured the northern Unity state capital Bentiu last week, another vital oil town.
According to the United Nations, about 400,000 civilians have fled their homes over the past month, many of them to escape a wave of ethnic violence between members of Kiir's Dinka people -- the country's largest group -- and Machar's Nuer community.