The Nigerian High Commission in South Africa had earlier notified nationals living in South Africa of possible violent attacks following inflammatory comments made online by South Africans against Nigerians.
The South African government has described safety concerns expressed by Nigeria as a false alarm.
"The Department of International Relations and Cooperation (DIRCO) has learned about an unfortunate advisory issued by the High Commission of the Federal Republic of Nigeria in Pretoria," the agency's spokesperson, Clayson Monyela, wrote in the statement.
PREMIUM TIMES reported that the Nigerian High Commission in South Africa had earlier notified nationals living in South Africa of possible violent attacks following inflammatory comments made online by South Africans against Nigerians.
DIRCO added that the advisory is regrettable, because it seems to create alarm and unnecessary tension between the citizens of South Africa and Nigerians living in or visiting South Africa.
"The South African national soccer team, Bafana Bafana, has played against their Nigerian counterparts, the Super Eagles, on many occasions, and there has been no history of soccer hooliganism among South Africans associated with the outcome of such encounters," it said.
The agency said it is confident that the sports-loving nation of South Africa poses no threat to Nigerian citizens, and does not agree with the apprehension expressed by the High Commission.
"As we have done in the past with similar alarming advisories, we call on the diplomatic representatives to approach DIRCO to address any concerns about diplomatic matters," DIRCO said.
Nigeria's Super Eagles will face the Bafana Bafana of South Africa later today in the semi-final of the African Cup of Nations (AFCON).