The migrants had set off in two trucks from Niger's northernmost mining town, Arlit, across the desert towards Tamanrasset in Algeria in mid-October but dispersed to find water after their vehicle broke down.
A senior military officer said: "We have discovered bodies scattered in various locations less than 12 miles from the border with Algeria."
Most were women and children. Their nationalities are not known.
Another military officer said about 20 people from the group survived the ordeal. Five of those walked for miles across the desert back to Arlit to raise the alarm.
The route across the Sahara is used by many migrants from the region and farther afield.
More than 32,000 migrants have arrived in southern Europe from Africa so far this year although hundreds who make it to the Mediterranean have drowned trying to cross in poorly-maintained boats.