The tropical cyclone that tore through Mozambique and other Southern African nations has spotlighted how the combination of rapid urbanization and climate change is turning deadly in some of the world’s poorest places.

The cyclone, which devastated towns and killed hundreds of people, is shaping up to be one of the worst weather-related disasters in the Southern Hemisphere, the World Meteorological Organization said Tuesday.

Since making landfall late Thursday with wind speeds of up to 105 miles an hour, the cyclone, dubbed Idai, has swept through coastal Mozambique before moving inland into Zimbabwe, where it has killed at least 98 people. In Mozambique, the official death toll climbed above 200, but President Filipe Nyusi warned that it could easily pass 1,000 as the scale of the damage was only becoming apparent. In the days before, flooding from heavy rain had killed at least 56 people in Malawi.

The Red Cross said that 90% of the Mozambican city of Beira, a port on the Indian Ocean with a population of around 600,000, had been destroyed. Aerial footage showed entire neighborhoods inundated and hundreds of buildings stripped of their roofs. Aid groups reported using limited numbers of helicopters to pluck people from trees and drop food to those they couldn’t reach. Elsewhere, volunteers were braving chest-high water to rescue residents trapped on high ground, rooftops and other elevated structures.

“The damage is so severe, because the affected areas are densely populated,” said Sergio Zimba, spokesman for Oxfam in Mozambique, one of dozens of charities scrambling to get help to the city. “Such disasters are more devastating in urban areas where basic infrastructure is absent.”

Tropical Cyclone Idai’s Path Wind speeds 56 mph 75 mph 37 mph Densely populated areas 100 miles Lilongwe 100 km mozambique malawi Idai’s path Quelimane Harare March 15 00:00 GMT March 16 March 12 12:00 GMT 00:00 GMT Beira March 13 zimbabwe 00:00 GMT March 14 00:00 GMT madagascar Mozambique Channel Wind speeds 37 mph 75 mph 56 mph Densely populated areas 100 miles Lilongwe 100 km mozambique malawi Idai’s path Harare Quelimane March 15 00:00 GMT March 16 March 12 12:00 GMT 00:00 GMT Beira March 13 zimbabwe March 14 00:00 GMT 00:00 GMT madagascar Mozambique Channel Wind speeds 37 mph 75 mph 56 mph Densely populated areas 100 miles Lilongwe 100 km mozambique malawi Idai’s path Harare Quelimane March 15 00:00 GMT March 16 March 12 12:00 GMT 00:00 GMT Beira March 13 zimbabwe March 14 00:00 GMT 00:00 GMT madagascar Mozambique Channel Wind speeds 37 mph 56 mph 75 mph Densely populated areas 200 miles mozambique 200 km malawi Idai’s path Harare March 15 00:00 GMT March 16 March 12 12:00 GMT 00:00 GMT Beira March 14 zimb. 00:00 GMT madagascar Mozambique Channel

The storm and the destruction it has left in its path have renewed questions about how poor countries with long coastlines are adapting to climate change—and whether the rest of the world is helping enough. Global climate deals, including the 1997 Kyoto Protocol and the 2015 Paris Agreement, promised help for developing nations to shore up infrastructure and other technologies to protect their populations from rising sea levels and other effects of changing weather patterns.

But the level of funding and speed of projects coming online are lagging behind, especially as populations grow in poor countries and become increasingly urbanized. The Green Climate Fund, established by the United Nations Framework Convention on Climate Change in 2009 to raise a significant portion of an overall funding goal of $100 billion a year by 2020 for climate-change adaptation and mitigation in poor countries, has so far received a mere $10.3 billion in pledges. It has started 102 projects, of which 43 are in Africa.

Beira, the city worst hit by Idai’s force, was in the middle of a World Bank-supported infrastructure upgrade to strengthen its defenses against flooding when Idai hit. The expansion of settlements in the city, many of them without formal electricity and sanitation systems, had left some 300,000 residents at risk of weather-related disasters, the World Bank warned in a report last year.

Residents search for bodies Tuesday in Ngangu township of Chimanimani after the devastation caused by Cyclone Idai. Photo: Zinyange Auntony/Agence France-Presse/Getty Images

The World Bank and other development institutions spent some $60 million on rehabilitating drainage systems in Beira to prevent flooding, and were planning to plant thousands of trees to delay water runoff. But the damage from the storm was worst outside the city center, which had been the focus of the project, said Michel Matera, senior urban specialist at the World Bank and the leader of the Beira project. Thanks to work already completed, damage from the storm was limited in the city center, said Michel Matera, senior urban specialist at the World Bank and the leader of the Beira project.

“We invested well, but the city is growing, the population is swelling, the adaptation project for Beira was not yet ready,” said Mr. Matera, adding that some $300 million was still needed to complete the project—a sum that was likely to rise following the destruction over the past week.

The World Meteorological Organization said the cyclone unleashed a record tide of 3.5 to 4 meters, which rose as high as 6 meters in some areas. “If the death toll reaches the levels suggested by the Mozambique president, then it will be the one of worst tropical cyclone disasters in the Southern Hemisphere,” said Clare Nullis, a spokeswoman for the Geneva-based body.

Satellite images released Tuesday by the European Union earth observation program Copernicus showed some 492 square kilometers underwater in Mozambique, and the Red Cross estimated that some 400,000 of Beira’s residents were now homeless. Medical charity group Doctors Without Borders said it had ceased all its medical activities in the city since last week, while the U.N.’s World Food Program warned that the cyclone could affect some 1.7 million people in Mozambique alone.

“It was like a war,” Nelson Moda, a teacher in Beira told the BBC. “We found a bathroom with no windows where we could be safe…I could see people dying and people crying and I couldn’t do anything. The house where I live has been destroyed.”

Similar flash floods have killed hundreds in Indonesia and other low-lying coastal parts of Asia in recent years, while deadly, rain-induced landslides in Africa often don’t even make the news. Increasingly, however, politicians in Africa say they want to work more closely together to shield themselves against the effects of climate change.

“This cyclone has come at a very huge human cost,” Nick Mangwana, Zimbabwe’s permanent secretary for information, said in a tweet Tuesday. “We certainly need a regional approach to these effects of Global Warming. These problems are transnational.”

Write to Nicholas Bariyo at nicholas.bariyo@wsj.com and Gabriele Steinhauser at gabriele.steinhauser@wsj.com

Corrections & Amplifications

The Green Climate Fund was established to raise a significant portion of an overall funding goal of $100 billion a year by 2020 to help poor countries adapt to and mitigate climate change. A previous version of this article incorrectly stated that the fund was supposed to raise that overall amount. (March 21, 2019)