A massive operation to repatriate thousands of Malawians faces a dual crisis: Durban's temporary processing site is overflowing, while a bus permit blunder has left hundreds stranded in Johannesburg.

Thousands of Malawian immigrants descended on a makeshift repatriation camp in Durban, where they were being verified and processed in what Home Affairs Minister Leon Schreiber described on Monday as "a heck of a big operation".

Meanwhile, about 500 people, who thought they were being repatriated to Malawi on four buses from Cape Town and three from Durban, were taken to Johannesburg instead, because the buses lacked the permits required to cross the border. They were dropped at the Malawian consulate in Sandton on the weekend.

Over the past week, Malawians began to gather outside a community hall in Sherwood, Durban, wanting to return to their country of origin. Many people have been evicted from their homes, lost their jobs, or faced threats of violence in the wake of March and March's anti-immigrant campaign.

As the number of people swelled, conditions deteriorated, with limited access to water, food or sanitation.

On Sunday night, those at Sherwood were transported to a new temporary repatriation location set up at Durban's Old Drive-In site.

Immigrants said the new site had more space and better living conditions.

"We are relieved because here we can at least use proper toilets and have a place...