Survivors said there were at least 180 people on board when the overloaded fishing vessel began to sink late on Saturday night near Tunisia's Kerkennah Islands off Sfax.
Local fishermen initiated the rescue and alerted the Tunisian Navy and the coast guard.
The death toll from the shipwreck is likely to be over 100 as some 60 of the boat's passengers are still missing at sea and presumed dead, UNHCR said.
The boat went down near the southern island of Kerkenna, overnight on Sunday.
"Among the 60 victims transferred to the forensic department at Habib Bourguiba hospital in Sfax, 48 are Tunisians".
IOM chief of mission, Lorena Lando detailed that it was reported that some 50 people had died on Sunday after it overturned while Sixty-eight others - from Tunisia and elsewhere - were rescued by the coast guards.
"The estimated 125 men, women and children drowned in waters off Turkey, Tunisia, Algeria, Spain and Morocco made 1-3 June the Mediterranean's deadliest for migrants this year", IOM said.
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"That's why UNHCR is advocating for safe routes for refugees to travel so that these unnecessary deaths don't take place".
UNHCR urged "durable" solutions for refugees and legal channels such as private sponsorship, family reunification and naturalisation.
Interior Ministry Spokesman Khalifa Chibani said Tunisian security forces intercepted eight individuals involved in planning this illegal transporting of migrants.
Meanwhile, survivors blamed the captain for abandoning the boat after it started sinking primarily for evading arrest by the coastguard.
Unemployed Tunisians and other Africans often try to depart in makeshift boats from Tunisia to Sicily in Italy.
An IOM statement added that "this tragedy occurs at a time when the organisation recorded the arrival of 1,910 Tunisian immigrants by sea, to Italy between 1 January and 30 April 2018, compared to only 231 migrants in the same period in 2017". The North African country's economy is in crisis since the toppling of autocrat Zine al-Abidine Ben Ali in 2011 threw Tunisia into turmoil with unemployment and inflation soaring.