Six survivors walked to a remote village where they said those they were travelling with, mostly from Ghana and Nigeria, died of thirst, according to Lawal Taher, the department head for the Red Cross in the Bilma region.
The Red Cross also said it has dispatched a team to the site “to gather information” on the circumstances.
Rhissa Feltou, the mayor of Agadez, a remote town on the edge of the Sahara that has become the smuggling capital of Africa, confirmed the death toll of 44, “for now”.
The journey from Niger to Libya is a primary route sub-Saharan African migrants take when trying to reach Europe.
In one of the most perilous parts of the trip across the Sahara desert, thousands of migrants each week are crammed into pick-up trucks for the days-long ride, often with only enough room for a few litres of water.
Authorities and aid organisations say while they are able to keep track of the thousands of migrant deaths in the Mediterranean Sea between Africa and Europe, it is almost impossible to know how many have died in the vast and unpoliced Sahara.
In early May, eight migrants from Niger, five of them children, were found dead in the desert while on their way to Algeria.
In a separate incident, soldiers on patrol in northern Niger rescued about 40 migrants from various west African countries who had been abandoned in the desert by people smugglers while travelling to Libya.