The IOM said in a statement
that 3,771 people died attempting to make the crossing on vessels last year -- a rate of more than 10 deaths each day.
By comparison, 3,279 migrant deaths were recorded in the Mediterranean in 2014.
More than three-quarters of the deaths, 77%, occurred along the central Mediterranean route, which was typically used by people smugglers operating from Libya's coast, the IOM said.
"It is shocking and inexcusable that desperate migrants and refugees have lost their lives in record numbers this year, when they should not," the IOM's Director General William Lacy Swing said in a statement. "The international community must act now to stop this trend against desperate migrants."
The deadly toll shows no sign of abating in 2016. On Tuesday, 24 migrants drowned off the coast of Turkey, in an apparent attempt to reach Greece, according to Turkish state media TRT. Thirteen people were rescued, TRT reported.
The victims were believed to have come from Iraq, Algeria and Syria, Turkey's semiofficial Anadolu news agency reported, quoting a Turkish official.
The number of migrants entering or attempting to enter Europe exploded last year, as the world witnessed an unprecedented surge of people fleeing wars, persecution and poverty in the Middle East and Africa.
Last month, the IOM said that the number of migrants who had entered Europe by sea and land during 2015 had passed the 1 million mark
, with the vast majority coming by sea over the Mediterranean.
Half of those making the crossing -- a half-million people -- were Syrians escaping the four-year civil war in their homeland, which has created what the U.N. calls the worst refugee crisis seen in 25 years. Afghans accounted for a fifth of the migrant flow, and Iraqis 7%.
The IOM said Tuesday that 1,004,356 migrants had made so-called "irregular arrivals" by sea in Europe in 2015 -- nearly five times the 2014 total of 219,000.
The organization said the deadliest month of 2015 had been April, when nearly 1,250 migrants died, mainly due to a capsizing in which an estimated 800 migrants drowned off the coast of Libya
. Only 28 people survived the incident, the IOM said.
Globally, the IOM said, there were an estimated 5,350 migrant deaths last year.
The second-deadliest region after the Mediterranean was in Southeast Asia, where thousands of Rohingya, a stateless Muslim minority fleeing persecution
in Buddhist-majority Myanmar, took to the sea in an attempt to reach Malaysia
and other countries.