Two witnesses alleged they were arrested by government soldiers along with an estimated 250 other men, herded into a police station in the capital Juba and then fired on.
The two witnesses, who were both wounded and managed to escape and take shelter at a UN base in Juba, said only 12 men survived the alleged massacre.
Testimonies from several other witnesses also paint a picture of a pattern of ethnically motivated violence, including killings and rape, since the fighting in the world's youngest nation started on December 15.
Kiir accused Machar of attempting a coup, while Machar says the president has exploited tensions within the army to carry out a purge. Rebels loyal to Machar have since seized control of several areas north of Juba, where ethnic killings are also reported to have taken place.
The two victims of the alleged massacre said they were targeted as members of the Nuer tribe, to which Machar belongs, and that the soldiers who carried out the killings were ethnic Dinka, the majority tribe to which President Kiir belongs.
AFP tried to visit the police station, situated in the Gudele neighbourhood, but was turned away by men in uniform and plainclothes forces. But the stench of death in the area was overpowering, with flies swarming around. The walls of the building were also riddled with holes.
Another ethnic Nuer man, who AFP will only name as Riek and who was also sheltering at a UN base in Juba, said he fled his job in South Sudan's presidential guard on Sunday after witnessing a week of killings and rapes and fearing his comrades would eventually turn on him.
Riek said that violent house-to-house checks were being carried out in Nuer neighbourhoods, and that anyone not answering the question "In choli" -- meaning "What is your name?" in the Dinka language -- would be dragged outside their home, tied up and shot.
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