His visit to the French overseas territory comes after Paris declared "exceptional natural disaster" measures for Mayotte late Wednesday night to enable swifter and "more effective management of the crisis".
Officials have warned that the death toll from the most destructive cyclone in living memory could reach hundreds -- possibly thousands -- as rescuers race to clear debris and comb through flattened shantytowns to search for survivors.
"The tragedy of Mayotte is probably the worst natural disaster in the past several centuries of French history," Prime Minister Francois Bayrou said.
Macron is expected to land in Mayotte around 10:30 am local time (0730 GMT), and will be travelling with "a very small delegation" to minimise the use of law enforcement resources needed elsewhere on the archipelago.
He will spend part of the day there, and will come with "four tons of food and health aid, as well as rescue workers", the French president said in a post on social media platform X early Thursday.
After an "aerial reconnaissance of the disaster area", Macron will go to the Mamoudzou hospital centre, according to an itinerary released Wednesday, to "meet with the healthcare staff and the patients being treated".
He will also visit a neighbourhood razed by the storm, meet with Mayotte officials, and is expected to outline a reconstruction plan.
A preliminary toll from France's interior ministry shows that 31 people have been confirmed killed, 45 seriously hurt, and 1,373 suffering lighter injuries.
But officials say the toll could rise exponentially.
Located near Madagascar off the coast of southeastern Africa, Mayotte is France's poorest region.
Besides declaring "exceptional natural disaster measures", authorities have also imposed a nightly curfew to prevent looting.
Cyclone Chido -- which hit Mayotte on Saturday -- was the latest in a string of storms worldwide fuelled by climate change, according to meteorologists.
Experts say seasonal storms are being super-charged by warmer Indian Ocean waters, fuelling faster, more destructive winds.
- 'It's chaos' -
An estimated one-third of Mayotte's population lives in shantytowns whose flimsy, sheet metal-roofed homes offered scant protection from the storm.
At Mamoudzou hospital centre, windows were blown out and doors ripped off from hinges, but most of the medics had taken to sleeping at their battered workplace on Wednesday as Chido had swept their homes away.
"It's chaos," said medical and administrative assistant Anrifia Ali Hamadi.
"The roof is collapsing. We're not very safe. Even I don't feel safe here."
But staff soldiered on despite the hospital being out of action, with electricians racing to restore a maternity ward -- France's largest with around 10,000 births a year -- to their proper state.
"The Mamoudzou hospital suffered major damage... Everything is still functioning, but in a degraded state," said the hospital's director Jean-Mathieu Defour.
In the small commune of Pamandzi, sheet metal and destroyed wooden structures were strewn as far as the eye could see.
"It was like a steamroller that crushed everything," said Nasrine, a Mayotte teacher who declined to give her full name.
With health services in tatters, and power and mobile phone services knocked out, French Overseas Minister Francois-Noel Buffet on Wednesday night declared "exceptional natural disaster" measures for Mayotte.
Under a new emergency system for overseas territories, the measures will hold for a month, and can be renewed every two months after that.
It will "enable the local and national authorities to react more quickly while streamlining certain administrative procedures", Buffet said.
- 'Massive support' -
Much of Mayotte's population is Muslim, whose religious tradition dictates that bodies be buried rapidly, meaning some may never be identified.
Assessing the toll is further complicated by irregular immigration to Mayotte, especially from the Comoros islands to the north, meaning much of the population is unregistered.
Mayotte officially has 320,000 inhabitants, but authorities estimate the actual figure is 100,000 to 200,000 higher when taking into account undocumented migrants.
French military planes have been shuttling between Mayotte and the island of La Reunion -- another French overseas territory to the east that was spared by the cyclone.
A "civilian maritime bridge" was launched between both island groups, said Patrice Latron, the prefect in La Reunion.
As of Wednesday, more than 100 tons of food was to be distributed.
"We're moving to a phase of massive support for Mayotte," he said, adding that around 200 shipping containers with supplies and water would arrive by Sunday.
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