Dikeledi hit the northern coast of Madagascar as a cyclone on Saturday evening before weakening into a severe tropical storm.

At 3.36 pm local time, the storm was 160 kilometres (100 miles) south of Mayotte, Meteo-France said in its latest situation report.

At its closest, Dikeledi passed around 100 kilometres south of the French territory early on Sunday morning.

"It is now moving away from the island," said Meteo-France.

On Saturday night, Mayotte was placed on red alert in anticipation of the storm's passage.

Dikeledi came less than a month after the most devastating cyclone to hit France's poorest department in 90 years caused colossal damage in mid-December, killing at least 39 people and injuring more than 5,600.

"In terms of impact, Antsiranana province in Madagascar has sustained the most intense conditions in recent hours," Meteo-France said, referring to the island's northern tip.

Three people died in the torrential rains that battered northern Madagascar, the National Office for Risk and Disaster Management (BNGRC) said on Sunday. More than 900 people were also affected.

Rain and wind intensified in Mayotte on Sunday morning.

"Gusts of up to 80-90 kilometres per hour are possible, particularly in the southern part of the island."

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.

Locals earlier said that they were concerned about the new storm's potential impact, given the devastation wrought by the cyclone in December.

- 'Very worried' -

"We're very worried, given what happened the first time," said Ali Ahmed, a resident of Mamoudzou, which is located on Grande-Terre, the main island of Mayotte.

The floods were reported in the south of the archipelago, devastating the village of Mbouini -- one of the few localities to have been spared by Cyclone Chido in December.

Torrential rain was reported in Pamandzi, in the south of the island of Petite-Terre.

Some locals were seen braving the red alert to shore up their roofs weakened by the rain.

Confined to their homes from Saturday night, inhabitants of Mayotte have been banned from moving around until further notice.

The archipelago was placed on red alert from 1900 GMT on Saturday. During the alert, all travel is banned except for rescue services and other authorised personnel.

But in Mamoudzou, locals were seen out on the streets, with some taking advantage of the rain to wash their vehicles.

More than 4,000 people have been mobilised in Mayotte, including members of the police and the military, France's interior ministry said.

Eighty accommodation centres have been set up to host some 14,500 people, the overseas territories ministry told AFP, saying that the situation was "calm".

The storm was expected to be reclassified as a cyclone again on Monday.

Over the next few hours, Dikeledi "will continue to intensify, possibly reaching the stage of an intense tropical cyclone as it turns southwards and then south-eastwards early next week", according to Meteo-France.

In the Comoros, heavy rain was expected during the day.

In Mozambique in southeastern Africa, Dikeledi could approach the coast of Nampula province on Monday.