The strongest cyclone ever to hit Mozambique has made landfall in the country’s north, five weeks after Cyclone Idai devastated its centre, according to meteorologists.

Surpassing both Idai and the 2000 cyclone that had been the strongest to date, Cyclone Kenneth hit Cabo Delgado province with wind speeds of 140km/h (87mph), bringing the threat of extreme rainfall.

After forming off Madagascar’s coast earlier this week, Kenneth passed to the north of the island nation of Comoros on Wednesday night, killing three people and causing widespread damage to homes and infrastructure.

The storm is expected to stall inland for several days and around one metre of rain is expected in the area north of the city of Pemba, more than the usual average for an entire year in the region.

The National Institute of Disaster Management said it would relocate rescue equipment including boats and helicopters from Beira, which was devastated by Idai. Some have been warning that southern Tanzania could be hit too, but the storm path appears to tend south.

Meteorologists said Kenneth was a category 4 hurricane on Wednesday night but had weakened slightly by the time it hit Mozambique. Cyclones of this magnitude are rare in the region, and two within just over a month was unknown until now.

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“It’s really an anomaly in the history of cyclones in this region. There’s never been two storms this strong hit in the same year, let alone within five weeks of each other in Mozambique,” said Eric Holthaus, a meteorologist who has worked in east Africa and was watching the cyclone’s path closely.

Holthaus said that there was probably a “blocking pattern” in the upper atmosphere that prevented Kenneth from dissipating inland or escaping to the south, so it would most likely sit around 100km inland, attracting more moisture from the Indian Ocean.

“Nothing like this has happened in this region, and rarely happens anywhere in the world, where a cyclone of this strength stalls for this many days. So the kind of rainfall totals that the models are showing for Kenneth are really extreme in the global context,” he said.

There is evidence, however, that blocking patterns such as the one that makes Kenneth so intense are getting stronger with climate change, he added. The rainfall, which could reach 1.5 metres in some areas, will be catastrophic for the people of northern Mozambique.

Volunteers from the Red Cross have spent the past few days warning people in the storm’s path and advising them to secure their roofs, put sandbags around their houses and get out of the area if possible.

“Most of these people are living in dire poverty ... so it’s not the case that they can just get in the car and drive 200km inland. They really are exposed,” said the Red Cross’s Matthew Carter, who was about to board a plane north from Beira, where aid workers are providing food, water, shelter and medicine to thousands of people made homeless by Idai.

The tropical cyclone could be accompanied by eight-metre waves and a three-metre storm surge.

The increased threat of diseases like cholera and malaria, as well as the availability of food, are major long-term worries that communities affected by both Kennegh and Idai face. Kenneth has hit at the peak of harvest season, meaning a possible six-month period without food.

“It’s not just the immediate effects of someone losing their home, it’s also the longer term effects of food price increases and lack of a harvest for farmers,” Carter said.

The Cabo Delgado region of northern Mozambique is not as highly populated as the area surrounding Beira, and the main coastal city, Pemba, is not expected to take a direct hit, so there may be fewer people directly affected than by Idai. But the country is struggling to deal with the after-effects of the first cyclone and has little capacity to tackle a new disaster.

Mozambique has had to take out a $118m (£91m) loan from the IMF in the wake of Idai, something that debt relief campaigners have called a “shocking indictment” of the international community, saying impoverished countries should be given emergency grants rather than having to borrow more money.