Malawi will join other countries in repatriating its nationals seeking to leave South Africa, where attacks on African migrants have been reported in parts of the country.

The Ministry of Foreign Affairs said in a statement late on Tuesday that the programme would be limited to citizens who have requested assistance, with details to be announced once logistical arrangements are finalised.

Xenophobic attacks are a recurring problem in South Africa, where immigrants are often blamed for economic challenges such as high unemployment.

Anti-immigrant groups have set a June 30 deadline for undocumented foreigners to leave, fuelling fear among migrant communities.

Mozambique said five of its citizens were killed in violence in the coastal town of Mossel Bay over the weekend, while Ghana repatriated hundreds of nationals last week.

South Africa's government has pledged to crack down on those perpetrating or inciting violence against migrants. President Cyril Ramaphosa told parliament on Tuesday that while tackling illegal immigration was important, the country should not resort to "violence, xenophobia and vigilantism."

South Africa has the biggest economy on the continent and is a destination for people from neighbouring countries seeking work. It also hosts refugees and asylum seekers fleeing conflict in countries like Democratic Republic of Congo.