The South African government says more than 53,000 foreign nationals have been deported or repatriated since launching a "migration management" campaign five weeks ago.

Most were from Malawi, Zimbabwe, and Mozambique, officials say, and the number is likely to rise as repatriations and deportations continue.

South Africa is carrying out one of its biggest crackdowns on undocumented migrants in years, following weeks of anti-immigration protests that have seen violence, intimidation and looting. 

Protesters have been demanding tighter border controls and mass deportations, accusing migrants of contributing to high unemployment, rising crime rates and collapse of public services.

The UN has warned against using migrants as scapegoats for South Africa's socioeconomic challenges.

Anti-migrant activists have threatened to stage weekly protests to pressure the government until their demands are met, and there are fears the protests could turn violent.

The demonstrators had set an "unofficial deadline" of 30 June for all undocumented migrants to leave the country, which has seen many foreigners leave to escape violence and intimidation.

Several countries, including Ghana, Nigeria, Uganda and Kenya, have flown their citizens home in recent weeks.

Justice and Constitutional Development Minister Mmamoloko Kubayi announced on Sunday that 53,499 foreign nationals have been processed for deportation and repatriation, "which is dominated by the Malawians, followed by Zimbabweans and Mozambicans".

"We are striving to achieve an orderly and regular migration which is mindful and sensitive to the concerns raised by our people, while observing human rights and dignity of all people in our country, irrespective of their citizenship and immigration status," Kubayi told a news conference in Pretoria.

She said the repatriation and deportation process has helped them catch people who were wanted by the police for alleged criminal activity. 

Authorities will continue to enforce its immigration laws, she added, but warned that protesters should not conduct unauthorised searches of homes and businesses that are suspected of sheltering undocumented migrants.

South Africa's President Cyril Ramaphosa has acknowledged public concerns about immigration but has condemned attacks against migrants, warning citizens against taking the law into their own hands.

South Africa is the continent's wealthiest nation and has long attracted migrants searching for better economic opportunities, some of whom enter the illegally.