They had made the long overland journey from Ethiopia, via Kenya and Tanzania, saying they are in search of jobs and better living conditions.
Some of the Ethiopians said they had been travelling for six weeks.
BBC reports one Simion Sidebo to have said he had paid more than US$3,000 to transporters.
Mozambican National Immigration Services spokeswoman Cira Fernandes said the Ethiopians had no passports or other documents.
Repatriations were costly: last year, the government spent more than $200,000 repatriating nearly 4,000 undocumented migrants, she said.
She however said that the UN’s International Organization for Migration (IOM) agreed to carry the cost of deporting the latest batch.
They flew back to Ethiopia from the capital, Maputo, and the IOM will help them “start up small-scale businesses to avoid becoming illegal immigrants again,” Fernandes said.