Citizens of a number of countries, including Ghana, Nigeria, Uganda and Zimbabwe, have fled South Africa since late May, after extremist groups intensified their crackdown on undocumented migrants and demanded that they leave the country.
Around 60,000 migrants have left South Africa since the beginning of June, according to the South African Border Authority.
More than half of them are Malawians, followed by Zimbabweans, Ugandans, Mozambicans and Kenyans.
Malawi's disaster agency says six people died of illness during the long and dangerous journey home.
"They were chased and moved from place to place and could not access their medicines and hospital care," the agency's commissioner Wilson Moleni told AFP.
