The migrants, most of whom came from West African countries, are believed to have died on June 3 after a sandstorm threw them off their route from the northern town of Arlit to Algeria, said Giuseppe Loprete, the IOM's chief of mission in Niger.
They were part of a wave of migrants trying to reach Libya to board smugglers' boats across the Mediterranean Sea into Europe.
"This tragedy highlights a feared but hitherto little-known danger too many migrants face long before they risk their lives at sea," said William Lacy Swing, the IOM's director general.
The dead included 17 men and one woman. They came from Niger, Mali, Ivory Coast, Senegal, Central African Republic, Liberia, Guinea and Algeria.
The route through northern Niger is heavily trafficked. In October 2013, Niger authorities recovered 92 bodies of migrants who died of thirst after the trucks they were travelling in broke down.
The IOM estimates that 1,865 people died this year through mid-June trying to cross the Mediterranean.
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