The boat had run into difficulty on Wednesday about 15 nautical miles off Libya and sent out a distress call, picked up by the coastguard in Catania in Sicily.
Two vessels - the MSF ship Dignity One and Irish patrol vessel Le Niamh - were immediately dispatched to the scene, but the boat capsized after the migrants all rushed to one side in anticipation of being rescued, the coastguard said.
Reports said that about 150 people were spotted in the sea.
Melissa Fleming, the Chief Communications & Spokesperson at UNHCR confirmed the reports, saying so far, 250 people has been rescued, 16 dead
Just in: Boat carrying 600 capsized off Libya. So far, 250 rescued, 16 dead. Worried for the others. Italian Coast Guard coordinating rescue
— Melissa Fleming (@melissarfleming) August 5, 2015
More than 2,000 people are estimated have died so far this year trying to make the perilous journey across the Mediterranean Sea to Europe.The International Organization for Migration (IOM) said on Tuesday that about 188,000 people have been rescued so far this year while trying to make their way to the old continent through the world's most dangerous migrant route.