Paramedics carry an injured survivor of a shipwreck to an ambulance at the port in Kalamata town. AP

At least 79 migrants drowned early on Wednesday and hundreds more were missing and feared dead after their overloaded boat capsized and sank in open seas off Greece, in one of Europe's deadliest shipping disasters in recent years.

Rescuers have so far saved 104 passengers, including Egyptians, Syrians, Pakistanis, Afghans and Palestinians.

“It’s one of the biggest operations ever in the Mediterranean,” Greek coastguard spokesman Nikos Alexiou told state broadcaster ERT TV. “We won’t stop looking,” he said.

Alexiou told local media on Thursday that all survivors are men. One of the dead, however, is a woman, said local reports.

“No other survivor has been found [besides the 104 rescued yesterday] and the bodies [recovered] also remain 79,” he added.

As a painstaking search for survivors continued, a European rescue-support charity said it believed around 750 people were on board the 20- to 30-metre-long (65- to 100-foot-long) vessel. The UN's migration agency estimated up to 400 while Greece declined to speculate on the passenger count.

By midday, 104 people had been rescued. A media report said the boat left Libya, and a shipping ministry official who spoke on condition of anonymity said most of those on board were from Egypt, Syria and Pakistan. There were even some Afghans.

Search and rescue operations were to continue through the night, with military aircraft deploying flares to light up the Mediterranean waters around the wreck site about 50 miles (80 km) southwest of the southern Greek coastal town of Pylos.

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Survivors were taken to the Greek port of Kalamata near Pylos. Covered in blankets, they rested on mattresses at a warehouse shelter, and the migration ministry was expected to move them to a camp outside Athens.

The shipwreck was the deadliest off Greece in several years. In February, 96 people died when their wooden boat smashed into rocks on Italy's Calabrian coast during a storm.

Greece's caretaker administration, in power between an inconclusive election on May 21 and new elections on June 25, declared three days of national mourning.

Migrants crowded on the decks

Greek state broadcaster ERT said the boat was en route to Italy from the Libyan town of Tobruk, which lies south of the Greek island of Crete. Greek authorities did not confirm the vessel's departure port.

An aerial view shows migrants onboard a fishing vessel in the waters off the Peloponnese coast of Greece. AFP

Alarm Phone, which operates a trans-European network supporting rescue operations, said it received alerts from people on board a ship in distress off Greece late on Tuesday, with erratic contact after that.

"According to the people, there were 750 people on board... We now hear reports of a shipwreck and fear they are true," it said on Twitter.

Greek coast guard spokesperson Nikos Alexiou, speaking to Greece's MEGA TV, said authorities did not know how many were on the boat, especially below deck, but reported it was crowded. "...There were too many people on the outer deck. It was full," he said.

The Greek coast guard said EU border agency Frontex first spotted the boat on Tuesday in international waters southwest of Pylos, and Italian authorities then alerted Greece to the vessel's presence.

Medical staff carry a survivor on a stretcher outside a warehouse at the port in Kalamata town. AFP

Alarm Phone said it informed Greek authorities, Frontex and the Greek division of the UN refugee agency UNHCR late on Tuesday afternoon.

The charity said that shortly afterwards, it spoke to people on the vessel who said the captain had fled on a small boat and appealed for help.

The Greek coast guard reported its agents approached the vessel and offered help. But migrants packed on its outer deck "refused assistance and stated their desire to continue their voyage", according to the coast guard.

In aerial images released by the coast guard, dozens of people on the boat's upper and lower decks were looking up with outstretched arms.

A few hours later, the vessel began veering from side to side before capsizing around 2 a.m. on Wednesday then sinking, a government official said.

Libyan smuggling networks

Greece is one of the main routes into the European Union for refugees and migrants from the Middle East, Asia and Africa.

Survivors of a shipwreck stand outside a warehouse at the port in Kalamata town. AFP

But since the previous conservative government of Kyriakos Mitsotakis introduced tougher controls at the country's migrant camps, more people have chosen to make a longer, riskier sea journey from Turkey to Italy via Greece.

The Greek migration ministry blamed international smuggling networks for putting migrants' lives at risk, while Filippo Grandi, the UN High Commissioner for Refugees, called on governments to work together on creating safe pathways for people fleeing poverty and war.

Libya, which has had little stability or security since a NATO-backed uprising in 2011, is a major launching point for people seeking to reach Europe by sea. People-smuggling networks are mainly run by military factions that control coastal areas.

In recent days, security forces in Libya have cracked down on migrants with detentions and deportations. It was not clear whether the ship that sank on Wednesday departed Libya before or after the crackdowns.

Survivors being taken to the Greek port of Kalamata near Pylos. AP

Numbers have fallen dramatically since a 2016 EU-Turkey deal to stem the flows.

About 72,000 refugees and migrants have arrived so far this year in Europe's front-line Mediterranean countries, according to United Nations data, with the majority landing in Italy and around 6,500 in Greece.

Nearly 1,000 people are estimated to have died or gone missing in the Mediterranean this year, according to the UN.

Agencies