South Africa has refuted claims that Nigerian nationals were killed in the latest wave of violence against immigrants in the country, further noting that a probe was underway into the deaths of two Mozambicans, a figure lower than the initial five reported by Maputo.

The Minister of International Relations and Cooperation, Ronald Lamola, in a statement late on Saturday, noted that reports that two Nigerians were killed in the chaos are "entirely unsubstantiated by available information."

"No Nigerian National has been killed during the current waves of attacks in South Africa," he wrote on his official X account.

"Second, it is untrue that five Mozambicans were killed. While there is an active South African Police Service investigation into the deaths of two Mozambican nationals, deaths we deeply regret, we trust that this matter will be thoroughly investigated, resulting in clear accountability and justice," he added.

Lamola's remarks were in response to Ghana's Minister for Foreign Affairs, Samuel Okudzeto Ablakwa, who accused Pretoria of lacking the political will to address the crisis.

"In our petition, we are demanding, first, a discussion of the matter. The South African government should explain to us why this keeps recurring and they don't seem to have the political will to deal with this decisively. Nobody is sanctioned," Ablakwa said in an interview with Joy FM.

Accra has filed a formal complaint against South Africa at the African Union seeking a discussion on the anti-immigrant violence.

The Ghanaian government argues that the violence contravenes the African Charter on Human and Peoples' Rights.

"We will vigorously defend any frivolous or baseless lawsuit emanating from Ghana against South Africa," Lamola said in his statement.

Lamola reiterated South Africa's earlier stance that majority of the Ghanaians that were repatriated to Accra were undocumented.

"We will not continue to tolerate these public spectacles, characterized by incomplete information and outright misinformation devoid of any diplomatic decorum," he said.

Besides Ghana, Nigeria is also preparing to repatriate its citizens from South Africa.

More than 1,000 Nigerians have already undergone screening for voluntary repatriation being facilitated by the Nigerian government, according to the Nigerians in Diaspora Commission (NiDCOM).

In April, the African Commission on Human and Peoples' Rights urged the South African government to accompany statements of condemnation with "prompt, concrete, and sustained measures to prevent recurrence and ensure accountability."