In a bid to avoid protesters expecting the flight to leave from Milan Malpensa Airport, the migrants were actually flown from Turin-Caselle, an airport over an hour away.
The deportation, the first of its kind in Italy, has been met with outrage.
Speaking to local media, protesters said: “We knew well two of the guys that were on that plane.
“Until yesterday they were in the Red Cross centre, they felt safe and they were preparing everything to ask for asylum.”
Italian officials are yet to comment on the deportation.
Alessandra Ballerini, a lawyer in Caritas Ventimiglia and expert in immigration law, said: “This is a mass deportation to a country where fundamental rights are violated and where their lives are in danger.
“With this operation, our country becomes an accomplice.”
In 2015, 60 per cent of Sudanese asylum seekers were granted humanitarian protection in Italy.