According to enca, a South African news agency, the embassy was closed on Wednesday.
“The decision to shut down the embassy is out of concern for the safety employees of the embassy,” enca quoted Lunga Ngqengelele from the Department of International Relations and Cooperation.
Reports indicate that protestors attacked the embassy but the extent of the damage is yet to be determined.
Ngqengelele told Eye Witness News that no one was injured during the incident.
It is believed that this was in retaliation to xenophobic attacks in South Africa that have affected Nigerians.
The Nigerian Government has however urged its citizens to desist from attacking South African organisations.
“The Federal Government has appealed to Nigerians not to attack South African companies operating in Nigeria in retaliation for the ongoing xenophobic attacks against Nigerians in South Africa,” a statement from the Information Ministry reads.
The Minister of Information and Culture, Alhaji Lai Mohammed, described as deeply disturbing the reports that some Nigerians, angered by the xenophobic attacks in South Africa, have started attacking South African companies in Nigeria.
According to him, investors in such companies, especially MTN and Shoprite, are Nigerians.
“Nigerian workers will be hardest hit if such companies are forced to shut down for fear of attacks,” his statement reads.
Nigerian police are said to have increased patrols outside embassies and foreign businesses.
The Information Minister added that they are taking decisive measures to push for an end to the xenophobic attacks against Nigerians in South Africa.
“President Muhammadu Buhari has dispatched a Special Envoy to convey to his South African counterpart, President Cyril Ramaphosa, his concerns and also interact with his South African counterpart on the situation,” he added.
On Wednesday, Nigerian VP Yemi Osinbajo said he would not be attending the World Economic Forum Africa in Cape Town.
enca news agency said over 1000 regional and global leaders were expected at the summit that begun on September 4.
“Clearly with this climate, he (Osinbajo) and Mr. President have agreed that he should not go,” Reuters news agency quoted Nigerian Foreign Minister Geoffrey Onyeama.