The island's authorities, Mayotte Prefecture, said they held a crisis meeting on Sunday to discuss the worsening unrest.
French President Francois Hollande earlier this month called the situation on the island "extremely worrying".
The latest flare-up saw groups go door to door in nine villages, according to the local authorities. Some families were immediately thrown out of their homes, while others were given ultimatums to leave within the coming days.
Nearly 700 people were expelled from the central village of Ouangani alone, including dozens of families with proof of legal residency, Comoran associations on Mayotte said.
Mayotte opted to remain under French rule when the other islands in the Comoros archipelago chose independence in 1975.
It is much wealthier than the neighbouring islands and more than 40 per cent of its population is thought to have been born abroad. Many have come from nearby Comoros in search of work.
For months, anti-foreigner groups have been whipping up hostility to migrants with leaflets accusing them of "clandestine immigration" and "daily thefts, assaults and murders".
The island's prefect, Frederic Veau, last week called for an end to the forced expulsions and said security forces could be deployed to maintain public order.
- with AFP