The group included 34 refugees, including 20 children, and perished between June 6 and 12, the interior ministry said on Wednesday.
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Nine of the adult bodies found in the desert of the landlocked West African country were women, Mr Mohammed said in a statement on television.
Only two – a Nigerian couple aged 26 – had been identified, he said.
“They probably died of thirst, as is often the case, and they were found near Assamaka”, a security source told AFP, referring to a border post between Niger and Algeria.
A government statement said they were found near the small desert town of Assamakka. This is the largest city in central Niger and the point at which buses end their routes and migrants are at the mercy of smugglers for the desert crossing to the Mediterranean coast.
Algeria is a main destination for refugees where in recent years thousands of people arrived from Mali and Niger.
Niger is one of the world’s poorest countries, and many here attempt to reach North Africa and Europe in search of work.
Two Nigerian migrants seeking greener pastures in Europe, via Libya, have died in the Sahara Desert, within the borders of Niger.
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IOM recorded 37 migrants died in the desert a year ago.
