The presidency said there was a need for the continental body to "intervene urgently," claiming that in the last two years "about 116" Nigerians had been killed, including 20 last year.
"This is unacceptable to the people and government of Nigeria," a senior presidential aide on foreign affairs, Abike Dabiri-Erewa, said in an emailed statement.
There was no independent verification of the claimed number of deaths, which may have been the result of wider criminal activities rather than anti-immigrant sentiment.
The community was hit badly by the wave of xenophobic violence that hit the country in April 2015 but South African police said only seven Nigerians died.
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An independent watchdog has said 640 people died from police brutality or in custody in South Africa.
Dabiri-Erewa renewed Abuja's call on the government in Pretoria to take "decisive and definite measures" to protect Nigerian citizens and other Africans in South Africa.
She said there was credible information that more attacks were being planned for Wednesday and Thursday.
South Africans police and government officials were not immediately available to comment.