Italian navy says at least 40 dead while hundreds of people were rescued, as it continues operation to save more.
Syrian refugees have boarded a ship on the Greek island of Kos for processing, hours after other migrants from Pakistan, Afghanistan and Iran clashed as they waited for their own paperwork.
Athens is struggling to cope with the European refugee crisis, which has seen tens of thousands of migrants try to make the dangerous crossings from the Middle East and North Africa to Europe.
The Greek government chartered the Eleftherios Venizelos ship to accommodate the Syrian refugees, who boarded the ship overnight, and whose asylum are being processed on the ship on Sunday.
The vessel is intended to ease the pressure on the island of Kos, which has found itself on the front line of the migrant crisis as people arrive in rubber dinghies at the rate of hundreds a day.
The huge passenger ship is ordinarily a car ferry which operates routes between the Greek islands and across the Adriatic to Italy.
As the Syrians are fleeing their country’s civil war, they being treated by Athens as refugees.
This gives them greater rights under international law than those from other countries regarded as economic migrants who have also crossed the narrow sea channel separating Kos from the Turkish coast.
Many of those arriving in Italy and Greece are intent on reaching northern Europe, and the priority of the authorities on Kos – which lies within sight of mainland Turkey – is to move them to other parts of Greece.
Another boat was preparing to take a load of Syrian migrants to the mainland but was yet to start operating.
The Greek government’s decision to give priority to Syrian refugees triggered clashes on Saturday, as other migrants complained about preferential treatment in processing.
Dozens of migrants from Pakistan, Afghanistan and Iran threw stones and exchanged blows outside the island’s police station as they waited to get the papers required for them to leave Kos for the mainland.
Al Jazeera’s Emma Hayward said that it was unclear who started Saturday’s clashes but “there was no holding back”.
“Anger, frustration and suspicion boiled over under the intensity of the summer sun,” she said.
The authorities said migrants of all nationalities would be processed.
A migrant camp on the island, run by Medecin Sans Frontieres (MSF) at the Captain Elias Hotel, provides basic facilities like mattresses and portable toilets but the organisation told the Reuters news agency they were struggling to cope with the number of arrivals.
Migrants, without food and water, have also been sheltering from the intense heat in tents and cardboard boxes.
On Tuesday, Greek police used fire extinguishers and batons against migrants after violence broke out in a sports stadium where hundreds of people, including young children, were waiting for immigration papers.
Nearly a quarter of a million migrants have crossed the Mediterranean to Europe this year, according to the International Organization for Migration.
Of these, about half have come to the Greek islands, with numbers surging in the summer when calmer weather makes the crossing less risky.
Elsewhere in Europe, commotion erupted in Macedonia, as hundreds of migrants fought to board a train for Serbia, which borders Hungary, an EU member state.
Migrants are trying to reach Hungary before it finishes building a fence designed to keep them out.