Some survivors and aid groups have described hasty burials, the stench of bodies and the devastation of precarious informal settlements whose population of migrants makes it even more challenging to determine the number of dead.
Mayotte, in the Indian Ocean off Africa's east coast, is France's poorest territory and a magnet for migrants hoping to reach Europe.
Already, France's interior minister this week has proposed cracking down.
The cyclone on Saturday was the deadliest storm to strike the territory in nearly a century.
It devastated entire neighbourhoods on the collection of islands with winds that exceeded 220km/h, according to the French weather service.
People in Reunion island are preparing goods for the victims of Cyclone Chido in Mayotte. (AP PHOTO)
Many people had ignored cyclone warnings, thinking the storm would not be so extreme.
Now residents pick their way across a landscape in search of food as telecommunications remain tenuous and even sturdily built structures including health centres have been damaged.
Dozens of French military personnel set up a makeshift camp at the airport.
French Prime Minister Francois Bayrou on Tuesday said more than 1500 people were injured, including more than 200 critically, but authorities fear hundreds and possibly thousands of people have died.
Local authorities could still confirm only 31 deaths on Wednesday.
On the French island of Reunion, about a three-hour flight away, loved ones were coming together to donate aid for survivors.
Some said their families in Mayotte had no food or water and roofs were blown off houses.
It had taken days to make contact with some.
"It is difficult because I feel helpless," 19-year-old Khayra Djoumoi Thany said.
Anrafa Parassouramin also has family in Mayotte.
"We are also afraid of disease outbreaks, because people are drinking water from wherever they can get it, and it's not necessarily potable water," she said.
Health Minister Geneviève Darrieussecq has raised concerns about the risk of a cholera epidemic on the archipelago which earlier this year had an outbreak of a highly drug-resistant strain of the disease.
French authorities said the distribution of 23 tonnes of water began on Wednesday.
The French minister for overseas matters, François-Noël Buffet, told French radio Europe 1 that aid brought by plane has started being allocated to locations across Mayotte.
The minister said the water supply system was "working at 50 per cent" and presented a risk of "poor quality".
Electricity had partially resumed.
A Navy ship was due to arrive in Mayotte on Thursday with 180 tonnes of aid and equipment, according to the French military.
French President Emmanuel Macron will travel to Mayotte on Thursday and visit a hospital and a destroyed neighbourhood, his office said.
"Our compatriots are living through the worst just a few thousand kilometres away," Macron said in a statement.
Some residents of Mayotte have long accused the French government of neglect.
On Tuesday evening, a program on public broadcaster France 2 raised 5 million euros ($A8.3 million) in aid for Mayotte through the Foundation of France charity, the channel said.
