South Africa has apologised to Nigeria for deporting 125 Nigerians from the country over their yellow fever vaccination cards.

Tensions between the two African powers escalated after 125 Nigerians were deported on arriving at Johannesburg's OR Tambo airport for allegedly carrying fraudulent yellow fever vaccination cards.

The move angered Nigeria who accused South Africa of breaching diplomatic protocol by failing to inform the Nigerian high commission of the deportations.

Nigerian foreign minister Olugbenga Ashiru also said the deportations were the result of xenophobia against Nigerian immigrants in South Africa.

Nigerian authorities reportedly retaliated by deporting at least 84 South Africans and the government asked from an official apology.

South Africa deputy foreign minister, Ibrahim Ibrahim, was quick to respond to the Nigerian demand telling reporters in Pretoria: "We apologise for this unfortunate incident and we hope this matter will not in any way affect our bilateral relations."

"We've put into place certain mechanisms to ensure this doesn't happen again, and we believe that this matter is closed," he added.

"We are in contact with the embassy in Nigeria, to see that there are no longer problems, and that any difficulties over vaccination certificates are dealt with before a visa is issued."

Ibrahim went further adding, "We understand the reaction of the Nigerian authorities."