UN diplomats said they had been told by sources in the capital, Juba, that the death toll was between 400 and 500.
South Sudan has seen two days of clashes following a reported coup attempt against President Salva Kiir Mayardit.
Fugitive opposition leader Riek Machar has denied government accusations that he tried to seize power.
“What took place in Juba was a misunderstanding between presidential guards within their division, it was not a coup attempt,” he told the Sudan Tribune, a Paris-based news website, in an interview published on Wednesday.
Riek Machar, a former South-Sudanese vice-president who fell out with President Salva Kiir in July, said he had no knowledge of or connection with any coup attempt.
President Salva Kiir has said a group of soldiers supporting Riek Machar had tried to take power by force on Sunday night, but were defeated.
Amid continuing clashes on Monday and Tuesday, the government said 10 senior political figures, including a former finance minister, had been arrested.
Details of the fighting have been sketchy, but a meeting of the UN Security Council in New York on Tuesday was told that the clashes were “apparently largely along ethnic lines”.
French UN ambassador Gerard Araud, who holds the rotating presidency of the Security Council, said up to 20,000 people had taken refuge in the UN mission in Juba.
He said the council had received only “patchy information” in a briefing given by UN peacekeeping chief Herve Ladsous.
The governor of Unity State, Simon Kun Pouch, was quoted on the government website as saying that the conflict had nothing to do with tribes.
“There are people out there saying what has happened is between the Dinka and the Nuer tribesmen. We the leaders of this country would want to state here that this is not true,” he said.
“If you see the people going with Dr. Riek [Machar], some are Dinkas, some are Chol, Nuer and other tribes,” he added.
The US has ordered all its non-emergency embassy staff to leave the country immediately.
President Salva Kiir said the clashes began when uniformed personnel opened fire at a meeting of the governing party, the Sudan People’s Liberation Movement (SPLM).
Fighting then continued into Monday when the government said it was back in full control.
However, fresh gunfire erupted on Tuesday near the presidential palace and many other areas of Juba.
Government officials say they are hunting for Riek Machar, who is believed to be in hiding.
Riek Machar – who leads a dissident faction within the SPLM – was thought to have escaped with some troops.
On Tuesday, the government said former Finance Minister Kosti Manibe, former Justice Minister John Luk Jok and former Interior Minister Gier Chuang Aluong were among the 10 people arrested.
Many were members of the cabinet that was sacked in its entirety in July.
South Sudan has struggled to achieve a stable government since becoming independent from Sudan in 2011.
The independence referendum was intended to end a decade-long conflict, led by the SPLM, against the north.
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