Mayotte was placed on red alert from 1900 GMT on Saturday in anticipation of the passage of Dikeledi, a storm forecast to skirt about 100 kilometres (62 miles) south of the territory.
It hit the northern coast of Madagascar as a cyclone on Saturday evening and weakened into a severe tropical storm, but is expected to regain intensity as it moves towards Mayotte.
It could be reclassified as a cyclone by Monday morning, according to French weather service Meteo-France.
Authorities called for "extreme vigilance" following the devastation wrought by Cyclone Chido in mid-December.
"Significant rain and wind deterioration is confirmed for the morning" in Mayotte, Meteo-France said in an update just before 6 am local time on Sunday (0300 GMT).
"Very heavy rains could generate flash floods," it warned, adding that "floods and landslides are expected in the coming hours".
It could also bring wind gusts of up to 90 kilometres per hour to the French territory, as well as "dangerous sea conditions".
Residents were advised to seek shelter and stock up on food and water.
"Nothing is being left to chance," Manuel Valls, France's new overseas territories minister, told AFP.
Cyclone Chido -- the most devastating storm to hit France's poorest department in 90 years -- caused colossal damage last month, killing at least 39 people and injuring more than 5,600.
Prefect Francois-Xavier Bieuville, the top Paris-appointed official on the territory, said Mayotte was placed on a red weather alert from 1900 GMT on Saturday to allow the public to take shelter.
"I have decided to bring forward this red alert to 10:00 pm to allow everyone to take shelter, to confine themselves, to take care of the people close to you, your children, your families," Bieuville said on television.
Messages in French and two regional languages were broadcast on radio and television to alert the population.
- 'Not fully recovered' -
More than 4,000 personnel have been mobilised in Mayotte, including members of police and the military, said the interior ministry.
The prefect has requested that mayors reopen accommodation centres such as schools and gyms that sheltered around 15,000 people in December.
He also ordered firefighters and other forces to be deployed to "extremely fragile" shantytowns in Mamoudzou and elsewhere.
Potential mudslides were "a major risk", the prefect said.
"Chido was a dry cyclone, with very little rain," he added.
"This tropical storm is a wet event, we are going to have a lot of rain."
Mayotte's population stands officially at 320,000, but there are an estimated 100,000 to 200,000 more undocumented residents living in shanty towns that were destroyed by the cyclone in December.
Mayotte resident Ismahane, who declined to provide her full name, said she was worried about the storm's potential impact, considering what Chido had done, and had stocked up on water, rice, canned goods, and "milk for the baby" ahead of Dikeledi's passage.
"We're still not fully recovered, and I don't know if we're going to make it or not," Ismahane told AFP.
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