Heavy rains pounded northern Mozambique on Saturday, fuelling fears of flooding two days after Cyclone Kenneth smashed into the coast, flattening buildings and knocking out communications.

The number of people killed has risen to five, a United Nations (U.N.) spokesperson said, citing the government. Aid agencies are struggling to assess the extent of the devastation as many areas remain cut off.

Cyclone Kenneth - packing storm surges and winds of up to 280 km per hour (174 mph) - is the second powerful storm to hit the impoverished nation within six weeks. It struck on Thursday night.

"(The) total in Mozambique is now five, according to the government," Saviano Abreu, spokesperson for the U.N. Office for the Coordination of Humanitarian Affairs (OCHA) in southern and eastern Africa said.

The cyclone killed three people in the Comoros before moving on to Mozambique, which is still struggling to cope with the impact of March's Cyclone Idai. Idai levelled the port city of Beira and brought floods that killed over 1,000 people across a swathe of southern Africa.

The World Food Programme has warned Kenneth could in the coming days dump twice as much rain on northern Mozambique, raising concerns of a repeat of the flooding in a region particularly prone to floods and landslides.

"Worryingly, it is still raining heavily," said Daw Mohammed, CARE's director of humanitarian operations, who is in the port city of Pemba, the provincial capital.

Downpours were particularly serious in areas north of the city, OCHA's Abreu said.

Almost all the homes on the island of Ibo were destroyed, government officials said on Friday, while the neighbouring mainland district of Macomia also suffered heavy damage. Around 18,000 people have been displaced.

A spokeswoman for the International Federation of the Red Cross and Red Crescent Societies (IFRC) said the organisation was also concerned about the coastal district of Mocimboa de Praia further north, because there had been no communication with the IFRC's team there.

Details about the full extent of the devastation were still scant as aid agencies struggled to reach or contact such areas, cut off by the storm. Many districts were without power.

The government and aid agencies said 30,000 people had been moved to safety before the storm struck, however it was estimated a total of almost 700,000 were at risk.

CARE said the government had set up 20 evacuation centres in Pemba, but planes were needed as many of the affected areas were not accessible by road.

OCHA posted a picture of a bridge that had been washed away, severing a main road that runs through Macomia. There were also reports of damaged houses in the district of Muidumbe, further inland, officials said, but aid agencies also said communications were largely down there.