BBC - Nigeria says two of its citizens have been killed in South Africa "at a time when foreigners are being unduly targeted" there.
A statement from the foreign ministry said Emeka Charles Iroegbu was "reportedly killed" on 28 June by police officers "using gruesome interrogation techniques", while unidentified assailants had killed shop owner Musa Yunana Joe on the same day.
The authorities in South Africa's capital, Pretoria, are yet to comment.
Nigeria's foreign ministry said the incidents came amid a rise in anti-migrant sentiment in South Africa, which has led to roughly 25,000 citizens from other African countries being repatriated by their nations, including some 700 Nigerians.
Protesters in South Africa have urged the government to do more to curb illegal migration. They say foreigners are taking jobs and unfairly benefiting from public services.
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In its statement, Nigeria's foreign ministry said Iroegbu was reportedly killed in Pretoria by officers from the Tshwane Metro police department.
Joe, killed on 28 June, was attacked outside his shop in the city of eMalahleni, the ministry said.
Abuja said it was placing the South African government "on notice" and that "all options remain on the table... if the uncultured and provocative trend of intolerance and apartheid-style behaviour of South Africa against foreigners is not addressed".
Nigeria has said it will seek compensation from South Africa for its citizens who have left the country, adding that Abuja had begun documenting businesses and properties left behind by Nigerians.
However, at a media briefing on Friday, South African cabinet minister Khumbudzo Ntshavheni said her government would not pay compensation and that Nigerians can sell registered properties they left behind on the South African market.
She also said: "We would be interested to know where the drug dens of Nigerians are, so they can show us where they have been holding the drugs so we can clean the drugs in South Africa quite urgently."
Nigeria's foreign ministry strongly condemned this comment in their statement on Sunday, calling it "unacceptable".
"Such derogatory, unprofessional and uncensored generalised public statements by highly placed government officials constitute hate speech," the ministry said.
Nigeria's foreign ministry also accused protest groups in South Africa, including March on March and Operation Dudula, of inciting violence and hatred against other Africans.
It warned that those responsible could face regional and international legal action, though it is unclear steps Nigeria would take and whether it plans to raise the issue with the African Union.
Some anti-migrant groups in South Africa had given undocumented foreigners a deadline of 30 June to leave the country.
Ghana, Malawi and Nigeria are among African countries which repatriated some of their citizens ahead of the deadline.
South Africa has one of the highest rates of unemployment in the world - at more than 30% - and anti-migrant sentiment has been rising in recent months.
The continent's most developed economy remains a magnet for people from poorer countries seeking work often in low-paid jobs.
