DURBAN - More than 100 Malawians are sheltering outside the Greyville Mosque in Marianhill, west of Durban.
They say they were forced to flee their homes overnight.
The group alleges they were threatened during a march in the area.
Landlords were also allegedly threatened.
The fallout from the 30 June demonstrations is unfolding at the Lebombo Border Post.
Migrants from across the country are arriving, hoping to leave South Africa as authorities ramp up repatriation efforts.
Deputy Police Minister Cassel Mathale is due to visit the border while scrutiny remains fixed on chronic security breaches.
The Inter-Ministerial Committee on Migration is visiting the repatriation centre outside Musina, Limpopo.
The centre was set up to verify the status of migrants before they return to their home countries.
The facility can accommodate up to 20,000 people.
At least 500 migrants have already moved to the centre.
Queues at the Home Affairs Repatriation Centre in Epping show no signs of easing.
Thousands of Zimbabweans are still waiting for buses to take them home.
More continue to arrive from farming communities across the Western Cape.
Malawian and Mozambican nationals have also joined the growing queues, placing even more pressure on the repatriation process.