The migrants, all of them men, had been arrested as they tried to cross Malawi heading to South Africa to seek work.
They were kept in crowded jails even after they had paid their fines or finished their six-month sentences because of a lack of funds to send them home.
“They have departed and we are thankful for the collaborative effort among various stakeholders,” Stephane Trocher, head of the International Organisation for Migration (IOM) in Malawi, told AFP.
“This was the initiative of the Ethiopian government.”
Most of the migrants had spent more than a year at Lilongwe’s notorious Maula prison.“About 50 to 70 Ethiopians still remain in Malawi until their documents have been finalized,” Catherine Sani, head of an NGO which has been advocating for the migrants’ release, told AFP.
Malawi says there has been a sharp rise in Ethiopians, Somalis and other Africans using the impoverished country as a transit route to seek work in South Africa.