Rebel fighters remain in control of Bentiu, capital of the oil-rich Unity State
Rebels in South Sudan have denied a UN report that they killed hundreds of civilians after taking control of the oil hub, Bentiu, last week.
Brig Lul Ruai Koang told the BBC there was a security vacuum after government forces left the town.
The UN said that civilians were killed along ethnic lines at a mosque, a church and a hospital.
More than a million people have been forced from their homes since fighting broke out in December 2013.
The conflict pits President Salva Kiir, an ethnic Dinka, against his former Vice-President, Riek Machar, from the Nuer community.
Although both men have prominent supporters from various communities, there have been numerous reports of rebels killing Dinkas and the army targeting Nuers.
But correspondents say that the killings in Bentiu are among the most shocking since the conflict began.
‘Piles of bodies’
The UN’s top humanitarian official in South Sudan, Toby Lanzer, told the BBC’s Focus on Africa programme that he had seen “piles of [the bodies of] people who had been slaughtered” last week.
He said they all appeared to be civilians.
Non-Nuer South Sudanese and foreign nationals were singled out and killed, the UN Mission in South Sudan (Unmiss) said.
Some 200 civilians were reportedly killed at the town’s Kali-Ballee mosque where they had sought shelter.
At the hospital, Nuer men, women and children, who hid rather than cheer the rebel forces as they entered the town, were also killed, it said.
The statement also said that hate speech had been broadcast on local radio stations, urging men to rape women from certain communities.
Many of those killed were Sudanese traders, especially from Darfur, Mr Lanzer said.
South Sudan analyst James Copnall says they could have been targeted because rebel groups in Darfur are alleged to back President Kiir against the rebels.
But Brig Koang told the BBC’s Newsday programme: “Our forces are not responsible for killing civilians anywhere in Bentiu.”
He suggested that government forces and their allies could have been responsible in order to make the conflict appear as though it was “tribal war”.
Upsurge in fighting
Bentiu, capital of the oil-rich Unity State, has changed hands several times during the conflict.
Control of the oilfields is crucial because South Sudan gets about 90% of its revenue from oil.
A ceasefire was signed in January but there has been a recent upsurge in fighting.
Last week, the UN said an attack on one of its bases in the central town of Bor in which at least 58 people were killed could constitute a war crime.
Fighting broke out last year after Mr Kiir accused Mr Machar of plotting to stage a coup.
Mr Machar, who was sacked as vice-president earlier in 2013, denied the charges but launched a rebellion.
The UN has about 8,500 peacekeepers in South Sudan, which became the world newest state after seceding from Sudan in 2011.