With no water or food, migrants are forced across the border at gunpoint in the searing heat.
The increase in deaths is thought to result from migrants taking more remote routes to avoid being caught.
Human rights abuses against migrants by traffickers and detention guards have been well documented in Libya, but new reports suggest the crisis is worsening.
Nearly 400 people have drowned trying to cross from Turkey to Greece by boat this year.
Half of the arrivals are fleeing war in Syria, according to the U.N.
The IOM estimates around 3,500 refugees have died while crossing the Mediterranean so far this year