SOS Mediterranée, which operates the Aquarius rescue ship alongside Médecins Sans Frontières (MSF), said it recovered two dead bodies from the bottom of an overcrowded inflatable boat.
Nearly 5,000 people died trying to cross the Mediterranean in 2016, the highest number on record, according to the IOM.
He added that the weather conditions are "extremely bad", speaking to The Independent. These children account for a staggering 91 per cent of all the 28,200 children who reached Italy's shores in 2016 as refugees or migrants.
The number of migrants who have reached Italy by boat from North Africa this year has already topped a previous record set two years ago, official data show, as pressure on Italy's shelter and asylum systems grows.
The boat is reported to have sank between Libya and Italy, about 30 miles from the Libyan coast.
"Current systems in place are failing to protect these children who find themselves alone in a totally unfamiliar environment".
The UN has said more than 5,000 people died in 2016 trying to cross the Mediterranean, majority on the Libya-Italy route.
He called for a coordinated European response given that the children were on the move.
It said that most of these unaccompanied children come from Eritrea, Egypt, Gambia and Nigeria, and a lot of them are boys between the ages of 15 and 17.
"The presence of so many unaccompanied or separated children along the Central Mediterranean route is unprecedented", said Melandri.
"IOM reports that 1,159 migrants and refugees entered Europe by sea in 2017, through 12 January, arriving mostly in Greece and Italy, compared with 22,590 through the first 12 days of January, 2016", the organization said.
Lucio Melandri, Unicef's senior emergency manager, said the findings indicated a "serious and growing problem" that Europe is failing to address.
Cristiano Ronaldo outshines Lionel Messi to bag Federation Internationale de Football Association best player award
Ronaldo won the old version of the award in 2008, and in 2013 and 14 when it was jointly organised with France Football magazine. Carli Lloyd of U.S. was named FIFA Women Footballer of the Year ahead of Melanie Behringer of Germany and Marta of Brazil.