"Unfortunately, we have now reached a milestone whereby over 2,000 migrants and refugees have died as of this past weekend," International Organization for Migration spokesman Itayi Virri told reporters in Geneva.
The organisation said around 188,000 people had been rescued so far this year trying to cross the Mediterranean, and warned the 200,000-mark could be crossed by the end of the week.
IOM said the latest toll confirms "this route as the deadliest for migrants in search of a better life," and warned the situation was worsening.
Nearly all of the people crossing the Mediterranean so far this year, often in rickety boats and at the mercy of human traffickers, have landed either in Italy (97,000) or Greece (90,500), the IOM said.
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Virri said the so-called central Mediterranean route had proved by far the deadliest, with just over 1,930 people dying trying to cross from Libya to Italy so far this year, while only about 60 had died trying to reach Greece.
Nineteen people lost their lives in the Channel of Sicily last week alone, with the bodies of 14 migrants brought to the Sicilian port of Messina on July 29. They had been travelling with 456 others who were rescued.
And yesterday, 550 migrants rescued in the Mediterranean over the weekend arrived in Sicily aboard a ship operated by Doctors Without Borders (MSF), which also carried the bodies of five people who died at sea.