The disease, also known as the Black Death, has killed at least 93 people and infected more than 1,300 - including 50 aid workers.
The tropical island is used to dealing with an annual outbreak, but this year’s epidemic has infected twice as many people and spread to Madagascar’s biggest cities for the first time.
And last year’s El Niño - dubbed ‘Godzilla’ because its unprecedented strength - could be to blame.
The weather phenomenon can cause big changes to climate around the world because of its impact on ocean currents and the distribution of warm water from the Pacific.Related articles
2016 was the strongest El Niño on record, and was nicknamed by some ‘Godzilla'
Professor Matthew Bayliss
Professor Matthew Bayliss, from Liverpool University’s Institute of Infection and Global Health, said the conditions created by the climate event may have resulted in the unusually severe plague outbreak.
He told MailOnline: “Our own research suggests that El Niño played a role of the Zika outbreak, but it is also possible that the conditions have facilitated this large scale plague outbreak.
“2016 was the strongest El Niño on record, and was nicknamed by some ‘Godzilla’."
A 2014 study by Professor Bayliss and climatologist Dr Cyril Caminade concluded Madagascar's plague season is linked with the phenomenon.
GETTYPlague latest: An unprecedented El Niño may have been responsible for the outbreak in Madagascar
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Workers cleaning and disinfecting the tents where patients sleep at the health center Plague