International Relations and Cooperation Minister Naledi Pandor has expressed her support for the closure of the South African High Commission in Abuja as well as the consulate in Lagos, Nigeria, as a precautionary measure.
However, according to a statement released on Thursday, Pandor "expressed her disappointment at having to take this decision".
In a statement released on Thursday, Pandor said both offices had closed on Tuesday following concerns reported to her by officials.
"This followed the receipt of threats against mission staff as well as the property of South Africa. After extensive consultations with relevant stakeholders as well as a security assessment of threats, the mission and the department took the decision to close the offices," the statement read.
It added while there had been no physical threat to diplomats or citizens, their safety was a priority.
The closure of these offices were therefore precautionary as the situation remained unpredictable, the statement read.
Pandor further lamented misleading information circulating on social media about a direct physical attack on the acting head of mission.
"These reports are totally false, as are reports of vandalism at the commission in Abuja and consulate in Lagos."
The statement added the acting head of mission was in contact with Nigerian authorities who were providing extra protection at the South African offices.
"The department has received reports of marches by demonstrators to South African companies as well as attempts to attack them. We are communicating with businesses that have branches in Nigeria and have requested their senior managers to remain in close contact with the department and ministry.
"It is established tradition in foreign policy that diplomatic missions should enjoy protection from the host country and while we remain perturbed at the threats directed at our missions, we are grateful to note that the security forces and government of Nigeria are upholding this long-established practice of foreign policy," the statement said.
Pandor also encouraged links between South African youth and Nigeria, saying South Africans should invite the Nigerian student association to visit the country.
"Meetings have been held at the mission with the student organisation and a committee was established to continue the dialogue and work on the details of the proposed visit," the statement said.
"The department and ministry will remain in constant contact with our representatives and will continue to assess the situation on the ground and provide feedback as new information becomes available."
Pandor is also set to meet the African heads of mission to South Africa next week.