Two diggers on Thursday morning demolished the shanties in the Longoni neighbourhood on the north of the island in less than an hour, AFP reporters at the scene said.
The prefect of Mayotte, Thierry Suquet, said the "small slum" was being cleared after a December court order to make way for a vocational training institute.
He told reporters that the settlement, which had once housed around 10 families, no longer had permanent inhabitants, and alternative housing had been offered to those using it as a temporary shelter.
Suquet also reported violence overnight in the main city of Mamoudzou, where police arrested one person after youths tried to set fire to "vehicles and buildings."
But 32-year-old Zarianti Bina told AFP the sudden demolition had come as a surprise.
"My mother lives here," she said.
"I only learnt they were coming yesterday. We have been contesting this for a year, but we got no prior warning."
"No solution has been provided," she added.
Operation Wuambushu ("Take Back" in the local language) has in recent days triggered clashes between youths and security forces on the French island and fueled political tensions with the Comoros.
Some 1,800 members of the French security forces - including hundreds from Paris - have been deployed
Around half of Mayotte's roughly 350,000 population is estimated to be foreign, most of them Comoran.
Mayotte is the fourth island of the Comoros archipelago, which was once a French territory.
France retained control over Mayotte after a 1974 referendum, but the island is still claimed by the Union of the Comoros, which gathers the three other islands.
It is France's poorest department with around 80 percent of the population living beneath the poverty line and high levels of social delinquency.
But it also benefits from French infrastructure, support and welfare, and this has encouraged an influx from the Comoros, whose nearest island, Anjouan, is 70 kilometres (45 miles) away.
Many migrants attempt the hazardous crossing on rickety boats used by smugglers.
