Ban urged international cooperation to help the region where he said 18 million people would be affected.
"Political turmoil, extreme climatic conditions and fragile economies are combining to create a perfect storm of vulnerability," he told a high-level meeting on the Sahel held on the margins of the 67th U.N. General Assembly.
Ban indicated the situation in Mali, with its extreme poverty, terrorism, insurgencies and organized crime, is ground zero for the crisis. More than 260,000 refugees have fled Mali into neighboring countries, putting further stress on those countries, he said.
But Ban said any military solution proposed for northern Mali should be thought through.
"This could have significant humanitarian consequences, including further displacement and restrictions on humanitarian access," he said.
Under a Security Council directive in July, the United Nations has been developing an integrated strategy for the region.