African Union (AU) forces had gathered in the Indian Ocean island nation of Comoros to support Comorian troops to take control of Anjouan and overthrow Bacar.
Bacar had been re-elected as president of the island lat year, but the result was never recognised internationally.
Mahamed Bacar Dossar, a senior government official, said: "French authorities have just confirmed to me that Mohamed Bacar is in Mayotte with 11 people.
"The Comorian justice system put out an international arrest warrant a long time ago. We will see whether the French authorities will respect it."
At least 11 people were wounded in the fighting as some Bacar loyalists took on the AU forces.
The central government says it will set up an interim administration for the island.
Since independence in 1975, Comoros has had 19 coups and attempted coups.