The European Union's anti-trafficking naval force in the Mediterranean, known as Operation Sophia, said there may be 20 to 30 fatalities from the latest sinking in the Mediterranean Sea, about 48 to 64 kilometers (30 to 40 miles) off Libya.
The Italian coast guard said it could not confirm the fatalities, but said it rescued 96 people from the vessel.
Those rescued were among more than 4,000 migrants rescued in the Mediterranean in 22 locations Thursday, it said.
The latest fatalities came a day after at least five migrants died off the Libyan coast when their ship rolled and then capsized. The incident occurred when hundreds of migrants rushed to the port side of the vessel as an Italian navy ship approached.
Rescuers used dinghies, a helicopter and another navy ship to save more than 560 migrants.
Shift in migrant route following EU-Turkey deal
The sinkings come as new figures reveal a dramatic recent shift in the migrant flow into Europe, with a surge of migrants entering Italy across the central Mediterranean.
The latest International Organization for Migration figures show the numbers of migrants entering Italy up 54% in the two weeks ending May 18, compared with the previous two weeks.
Over the same period, migration to Greece -- the main entry point for the bulk of illegal migrants into the European Union -- has dropped 67%.
The organization attributes the change to a deal between Turkey and the European Union
to try to control migration through Turkey into Greece, which it said has "brought migration flows through the Eastern Mediterranean and the Western Balkan route to a standstill."
For every Syrian sent back to Turkey under the plan, a vetted Syrian refugee would go from Turkey to Europe to be resettled, with a cap of 72,000 people.
In return, the European Union would give additional funding to refugee-specific projects in Turkey and grant visa-free travel to Turkish nationals
The figures show there have been 174,395 irregular arrivals into Europe in the first quarter of this year, more than eight times the number in the same period last year.
However, migration to Italy remains lower than it was at the same period a year ago -- with the spike in arrivals into Greece earlier in the year accounting for the much higher immigration numbers into Europe so far in 2016.
Greek migrant camp emptied
The U.N. refugee agency confirmed Thursday that an overwhelmed migrant camp on Greece's border with Macedonia has been completely cleared.
More than 10,000 migrants had been staying at Idomeni camp, a facility only equipped to house 2,400, with thousands stranded there in deteriorating conditions since Macedonia shut its border in March
, sealing shut the main immigrant route to Western Europe.
Conditions at the camp were dire, with the U.N. refugee agency saying in March that many residents, about 40% of whom were children, were suffering from respiratory problems.
Greek officials have been relocating the residents to more organized facilities
in other parts of the country.
Medical charity Doctors Without Borders, which has been providing health care and psychological support in the camp, condemned the clearance, and called on authorities to provide migrants with more information about their destinations.
"People are not being informed of where they are going and this is far from acceptable," Michele Telaro, the group's project coordinator in Idomeni, said in a statement.
"They need to be able to make informed decisions, and they must be provided with accurate information in order to do so. They have already fled conflict and violence and spent more than two months living in unacceptable conditions in Idomeni."