Images from Mayotte, which like other French overseas territories is an integral part of France and ruled from Paris, showed scenes of devastation, with homes reduced to piles of rubble.
The crisis, which erupted at the weekend the day after President Emmanuel Macron appointed Francois Bayrou as the sixth prime minister of his mandate, poses a major challenge for a government still only operating in a caretaker capacity.
The cyclone left health services in tatters, with the main hospital extremely damaged and health centres knocked out of operation, Health Minister Genevieve Darrieussecq told broadcaster France 2.
"The hospital has suffered major water damage and destruction, notably in the surgical, intensive care, maternity and emergency units," she said, adding that "medical centres were also non-operational".
Macron was due to chair a crisis meeting in Paris at 1700 GMT, the Elysee said.
Interior Minister Bruno Retailleau, whose super ministry is responsible for Mayotte, arrived on the island to oversee rescue efforts.
"In reality for the toll we are going to need days, days," he told officials after arriving, warning against giving any figures at this stage.
Chido is the latest in a string of storms worldwide fuelled by climate change, according to experts.
The "exceptional" cyclone was super-charged by particularly warm Indian Ocean waters, meteorologist Francois Gourand of the Meteo France weather service told AFP.
Cyclone Chido caused major damage to Mayotte's airport and cut off electricity, water and communication links when it barrelled down on Saturday.
Trees have been uprooted and power lines knocked down, while supplying fresh drinking water, a problem on Mayotte even in normal times, is now a major priority.
- 'Shanty towns flattened' -
Asked about the eventual death toll, Prefect Francois-Xavier Bieuville, the top Paris-appointed official on the territory, told broadcaster Mayotte la Premiere "I think there will definitely be several hundred, perhaps we will come close to a thousand or even several thousand".
With roads closed, officials fear that many could still be trapped under rubble in inaccessible areas.
The overwhelming majority of Mayotte's population is Muslim and religious tradition dictates bodies must be buried rapidly, meaning some may never be counted.
Mayotte is France's poorest region with an estimated third of the population living in shanty towns whose flimsy sheet metal-roofed homes offered scant protection against the storm.
"All the shanty towns are flattened, which suggests a considerable number of victims," a source close to the authorities told AFP, asking not to be named.
And assessing the toll is further complicated by the illegal immigration to Mayotte especially from the Comoros islands to the north.
Mayotte officially has 320,000 inhabitants, "but it is estimated that there are 100,000 to 200,000 more people, taking into account illegal immigration," added the source.
The source said few unregistered residents would have gone to the accommodation centres before the cyclone, "probably for fear of being checked."
- 'Apocalyptic scenes' -
Chido was packing winds of at least 226 kilometres (140 miles) per hour when it slammed into Mayotte, which lies to the east of Mozambique.
The mayor of Mayotte's capital Mamoudzou, Ambdilwahedou Soumaila, told AFP the storm "spared nothing".
"The hospital is hit, the schools are hit. Houses are totally devastated," he said.
One resident, Ibrahim, told AFP of "apocalyptic scenes" as he made his way through the main island, having to clear blocked roads himself.
The nearby French island of La Reunion was serving as a hub for the rescue operations. Hundreds of French security personnel are being deployed to take part in the effort.
As authorities assessed the scale of the disaster, a first aid plane reached Mayotte on Sunday.
It carried three tonnes of medical supplies, blood for transfusions and 17 medical staff, according to authorities in La Reunion.
Ousseni Balahachi, a former nurse, said some people did not dare venture out to seek assistance, "fearing it would be a trap" designed to remove them from Mayotte.
Many had stayed put "until the last minute" when it proved too late to escape the cyclone, she added.
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