Thousands at risk in Mozambique as heavy rains predicted in wake of Cyclone Kenneth

Serious flooding has hit parts of northern Mozambique, just days after Cyclone Kenneth tore through the area, completely flattening many communities and leaving thousands at risk.

At least five people have died and almost 160,000 people could be at risk, with many left exposed and hungry as waters rise.

The government is urging people to immediately seek higher ground, with more rain forecast for the coming days.

Aerial footage filmed by the World Food programme showed parts of the region's main city, Pemba, submerged in waist-deep water.

Hundreds of thousands of people are again at risk in the country just six weeks after Cyclone Idai ripped into central Mozambique and killed more than 600 people with flooding.

Heavy rains are expected in the next few days. Credit: AP

Yet the remnants of Cyclone Kenneth - a Category 4 hurricane which hit the country on Thursday - could dump twice as much rain as Idai, the UN World Program has said.

As much as 250 millimeters (nine inches), or about a quarter of the average annual rainfall for the region, had been forecast over the next few days.

More than 35,000 homes in parts of Mozambique's northernmost Cabo Delgado province were partially or fully destroyed by the storm.

In Cabo Delgado, the International Federation of Red Cross and Red Crescent Societies reported heavy damage, with the communities of Macomia, Quissanga and Mocimboa da Praia of highest concern.

A man finds his way around a destroyed docking bay on the coast of Pemba. Credit: AP

As water levels continue to rise, Mozambique authorities have asked residents the of Mecufi and Chiure districts, and parts of Macomia and Muidumbe districts to immediately seek higher ground.

"I have never seen such rains in my life," said one Pemba resident, 35-year-old Michael Fernando.

Houses in the region have begun to collapse due to the rains, and a UN rescue team has been mobilised.

"We are unfortunately expecting devastating floods," the UN humanitarian agency said in a tweet.

Community members look at rubble and other items washed close to their doorstep when Cyclone Kenneth struck. Credit: AP

This was the first time in recorded history that the southern African nation has been hit by two cyclones in one season, again raising concerns about climate change.

"There's a very intense strip of destruction where the wind first made impact in coastal districts," Nicholas Finney, response team leader with the aid group Save the Children, told The Associated Press after visiting Macomia district.

The team found people in shock in a region where a cyclone had never been recorded in the modern age.

Terrified children and traumatised parents "face a huge task to start to rebuild", he said.

Children play outside a school that had its roof destroyed. Credit: AP

Rain is forecast over the next several days and Mozambique's meteorological authority said the storm could potentially move back out to sea and intensify again, Mr Finney added.

"It doesn't look good, quite honestly," he said of the risk of flooding.

The two cyclones mean many livelihoods have been lost across the country, leaving people wondering how they will cope in a country struggling with one of the world's highest poverty rates.