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WHO Director-General Tedros Adhanom came up with the warning at a regular briefing on Friday.
"The pandemic, and the restrictions put in place to suppress it, are taking a heavy toll on 220 million people in protracted emergencies," he said.
He called upon the world not to focus entirely on COVID-19 at the expense of other crises battering the world.
"Many countries, especially in Africa and the Middle East, are still reeling from years of conflict and other humanitarian crises. COVID-19 threatens to exacerbate many of these crises," he said.
Since its outbreak, the pandemic has disrupted many aspects of life, including education, travel, agriculture and more.
Many countries around the world have projected slumps in their economies as the pandemic continues to batter their borders.
Governments have been forced to re-focus funds towards the fight against COVID-19, leaving other sectors ailing.
In his address on Friday, Tedros urged countries to strengthen their health systems to better tackle any future crises.
"The pandemic is teaching us that health is not a luxury item; it's the foundation of social, economic and political stability," he said