"Last Saturday, 80 migrants were saved in the desert, 382 kilometers (237 miles) from the town of Agadez," the IOM's Niger office said on Facebook.
"Sadly, two others died from extreme dehydration."
The refugees had been heading to Libya, the crossing point for the hazardous voyage to Europe, when their vehicle broke down and they were "abandoned by their smugglers," the IOM said.
They were stranded for three days before help arrived, Presstv reported.
The agency says it has helped to save more than 3,000 people this year through search-and-rescue teams, run with Nigerien NGOs, which comb the desert for stranded refugees.
On May 22, the IOM, a UN-related organization, said 386 refugees had been picked up in a rescue operation the previous week between Arlit and Assamaka, a town on the border with Algeria.
Niger has become one of the main routes for poor refugees heading north to the Mediterranean coast in the hope of crossing to Europe.
The Saharan route is notorious for its dangers, which include breakdowns, lack of water and callous traffickers who abandon refugees in the desert.
In 2015, Niger introduced a law making people-smuggling punishable by a jail term of up to 30 years. The armed forces, for their part, have also stepped up patrols in the desert.