An estimated 10,000 migrants have died or gone missing in the Mediterranean since the start of 2014, the UN refugee agency (UNHCR) and the International Organization for Migration (IOM) said Tuesday in Geneva.

UNHCR counted 3,500 dead or missing in the Mediterranean Sea in 2014, when the number of refugees fleeing Syria for Europe began to soar.

Last year 3,771 died, while an additional 2,800 people lost their lives between January 2016 and the beginning of June as they tried to find refugee protection or better livelihoods in Europe.

More than 330 people are currently feared dead in the latest major Mediterranean shipwreck off the Greek island of Crete last week, the aid and advocacy group IOM said earlier on Tuesday.

Several survivors have told IOM staff that the vessel was carrying 650 people when it sank Friday en route from Egypt to Italy.

In addition to nearly a dozen corpses that were recovered last week, 320 people remain missing and are presumed to have drowned, spokesman Joel Millman reported.

One 3-year-old girl survived because her father entrusted her to another migrant, asking him to look for her relatives in Egypt.

The girl's father, mother and two brothers died, the migrant told IOM staff after he was rescued along with other survivors.

Millman said there was a sharp rise in children trying to cross the sea to join family members who are already in Europe.

"Visa processes take a long time, so there is a strong urge to give your children into the hands of smugglers," he said.

The biggest national groups arriving in Italy are from Eritrea, Nigeria and Gambia, while those who have reached Greece this year were mainly from Syria, Afghanistan or Iraq.

Meanwhile in Greece, the main gateway to Europe for migrants last year, the authorities revised the number of people registered on its soil upwards by nearly 10 per cent.

The body in charge of migrants attributed the rise to the first-time inclusion of migrants staying in UN-run camps.

With that, the number of registered refugees and migrants rose to 57,458, some 7,500 of whom are sheltered in the so-called hotspots on Aegean islands.

They have been stranded in Greece since March, when neighbouring Macedonia followed the example of other countries further north by sealing its border to migrants.

That same month, the European Union and Ankara agreed to send new arrivals back to Turkey. In return, the bloc has said it will resettle Syrian refugees directly from Turkey, but there has been slow progress on this side of the deal in practice.

The number of arrivals from Turkey to Greek islands has declined dramatically since, from highs of thousands each day to one or two dozen.

Over 1 million migrants and refugees made it to Europe's shores over the course of 2015, followed by more than 206,000 arrivals since the beginning of this year, according to a UN tally.

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