The survivors of the first shipwreck, which happened yesterday, said some 650 people were aboard their boat when it left chaos-wracked Libya.
But they "spoke of 100 missing people who were stuck in the hull," a spokesman for the International Organization of Migration in Italy, Flavio Di Giacomo, told AFP. Italian authorities had initially given a toll of five confirmed dead.
While the Italian navy was able to rescue some 560 people from the water yesterday, the shipwreck may be one of the worst tragedies in the Mediterranean in recent months.
Several rescuers from the Italian navy jumped into the water in an effort to help, some grabbing people by the hair in order to pull them to safety.
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Separately, the EU's naval force announced that up to 30 migrants were believed to have died after another ship flipped over today, drawing rescuers to the scene who threw life jackets and floats to those in the water.
The single deadliest migrant boat sinking remains one from April 2015 when some 700 people died.
Amid the catastrophes at sea, police in Greece were finishing the evacuation of the squalid Idomeni refugee camp on the border with Macedonia that had become a symbol of human suffering and chaos as Europe struggles with its worst migrant crisis since World War II.
In the space of three days, police transferred about 4,000 migrants by bus from Idomeni to newly created camps in the industrial outskirts of Greece's second city Thessaloniki.
The muddy, overcrowded Idomeni camp exploded in size after Balkan states began closing their borders in February to stem the human tide seeking new lives in northern Europe.
As the footage of yesterday's capsise went around the world, photographs posted on social media showed migrants from Thursday's shipwreck waving their arms for help as they balance perilously on the deck of the boat, already underwater but still clearly visible.