Cyclone Kenneth battered northern Mozambique on Thursday with gusts of up to 280 km/h after killing three people on the island nation of Comoros overnight.

Impoverished Mozambique is still recovering from another powerful tropical cyclone, Idai, which made landfall further south last month, flattening the port city of Beira and killing more than 1,000 people across a swathe of southeastern Africa.

A regional cyclone-monitoring centre on the French island of La Réunion said Kenneth made landfall at around 4:30 p.m. local time north of the port city of Pemba and was expected to weaken as it moved inland.

The storm caused storm surges of up to five metres in some areas and rains associated with it could cause serious flooding, the centre said.

A child is transported on a fridge during floods after Cyclone Idai, in Buzi, outside Beira, Mozambique on March 21. (Siphiwe Sibeko/Reuters)

This is the first time in known history that Mozambique has been hit by two cyclones in one season, United Nations spokesperson Stephane Dujarric told reporters in New York.

The new cyclone threatens an area of Mozambique where residents are not used to such strong storms, UN officials said. That includes Cabo Delgado province, which has seen a rise in deadly militant attacks in recent months.

Mozambican officials said, in all, more than 680,000 people were at risk from Kenneth. There were concerns that five rivers and coastal waterways could burst their banks, leading to severe flooding.

A video posted by Mozambique's disaster management office showed director Augusta Maita warning residents that the new storm could be as strong as Cyclone Idai. Compulsory evacuations of buildings began for some families, the office said, sharing a list of shelters that were mostly local schools.

"We've already evacuated 30,000 people from the areas likely to be hit by the cyclone. The compulsory evacuation process will continue until we have all people in secure ground," spokesperson Paulo Tomas said.

The agency said it had supplies ready to assist 140,000 people for 15 days.

The UN called Idai "one of the deadliest storms on record in the southern hemisphere," and another major storm again raised concerns about climate change. Low-lying Mozambique's 2,400-kilometre Indian Ocean coastline makes the country one of the world's most vulnerable to global warming's rising waters.

As it approached Mozambique, Cyclone Kenneth left people in the Indian Ocean island nation of Comoros without power, with some losing their homes. The UN said it was still assessing the extent of the damage.

A man stands on fallen trees which damaged his home in Moroni, Comoros, Thursday, after Cyclone Kenneth hit the island nation. (Anziza M'Changama/Associated Press)

In Tanzania, the government told students and workers in the southern regions of Lindi, Mtwara and Ruvuma to stay home but said people living near the coast should leave.

Cyclone Kenneth is expected to linger over Mozambique, dumping rain until late Monday evening and bringing the risk of more intense flooding, said Dipuo Tawana, forecaster at the South African Weather Service.

In neighbouring Zimbabwe, where hundreds died in heavy rains following Cyclone Idai, the civil protection department sent out a warning that some areas near the eastern border with Mozambique could be affected by the cyclone.

The UN, the Red Cross and other aid organizations were bracing for what could be another large relief operation, again in mostly rural areas. The UN already had expressed concern that its $458-million aid appeal for what will be months of Cyclone Idai relief work in Mozambique and neighbouring Zimbabwe is just 24 per cent funded.

"Although floodwaters have receded in most areas affected by Cyclone Idai, access is still a challenge as infrastructure was severely compromised," UN World Food Program spokesperson Herve Verhoosel said in a statement. "Another storm would be an additional blow for the people of Mozambique and further complicate the response in all areas."

He said the agency has 300 tonnes of "food commodities" already positioned in Mozambique's northern coastal towns of Palma and Mocimboa da Praia and that its local partner has been told to protect the warehouses to "weather the storm."

The effects of Cyclone Idai will likely be felt for months, if not years. Even as authorities say a cholera outbreak is being contained, malaria is a growing concern. More than 14,800 cases have been reported since March 27 in the hard-hit province of Sofala alone, the UN children's agency said.