More than 500 homes have been destroyed by downpours and at least 53 people have been killed by landslides over the weekend in Rwanda, officials say.
The BBC reports that the downpours has damaged infrastructure across the country, especially in the north.
Officials have said the the northern Gakenke district has been the hardest hit, with at least 34 deaths.
This comes a just over a week after a deadly building collapse in Kenya, after days of flooding, killing at least 50 people.
While in the coastal city of Mombasa, a six-storey building extension of a shopping center also collapsed this week.
Experts are blaming the El Nino weather phenomenon for catastrophic incidents in four East African countries, Deutsche Welle reports.
El Nino-induced rainfalls have already wrecked havoc in Kenya, Ethiopia, Tanzania, and now Rwanda, while Southern Africa has also been hit, output of the staple maize crop cut has been nearly halved.
While Rwanda is used to experiencing landslides, experts say due to El Nino, the effect is different this time around - at least 67 people have been killed from January to April, international media reports.
The World Food Program said on Monday that El Nino is progressing toward a potential "regional emergency" which may require a coordinated international response.
In the southern regions of Ethiopia, floods and failed rains have led to crops failure. The United Nations reported that a year of drought had pushed about 10.2 million Ethiopians into dire conditions needing food aid to survive, Deutsche Welle reports.
El Niño affects rainfall patterns and temperatures across the globe, but most intensely in the tropical regions of Africa, the Asia-Pacific and Latin America.