The migrants are believed to have been hoping to travel on to Europe and were discovered by a military patrol several days ago, the source said.
"The migrants were subjected to terrible torture by their smugglers, before being abandoned without food or water," reported the online newspaper Air Info, based in the remote town of Agadez, citing a security source.
The migrants were saved close to the arid dusty town of Achegour, the paper said, a transit point for migrants seeking work in Libya or trying to reach the sea to sail to Europe.
Temperatures in Agadez currently hover at around 40 degrees Celsius (104 degrees Fahrenheit) but have hit almost 50 degrees Celsius in the past.
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Last year, the International Organisation for Migration (IOM) recorded 335,000 migrants heading northwards out of Niger.
Many perish while trying to cross the desert in crammed pick-up trucks with often meagre provisions of water, as jerrycans carrying fuel take priority.
Germany and Italy last month called for an EU mission to be installed on the border between Libya and Niger to reduce the migrant flow.
To fight against people smuggling, the Niger government in 2015 passed a law banning the illegal trafficking of migrants with those found guilty facing a prison sentence up to 30 years.