"You've now had since the start of 2014 -- when this phenomenon of rising numbers across the Mediterranean happened -- 10,000 deaths. That threshold has been crossed just in the last few days," UN refugee agency spokesman Adrian Edwards told reporters.
UNHCR said the number of Mediterranean deaths had risen sharply in 2016, with 2,814 people dying since the start of the year, following a total of 3,771 in 2015 and 3,500 the year earlier.
That amounts to 10,085 deaths in less than two and a half years.
"It's an extremely worrying dynamic," he said, reiterating the agency's call for the world to find "viable alternative and regular means of dealing with these movements".
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"They're happening, they're not stopping, they need a solution to prevent further lives being lost," he said.
The International Organisation for Migration meanwhile said the death toll so far this year was already nearly a thousand above the 1,838 deaths registered in the Mediterranean during the first half of 2015.
Following the latest shipwreck off the Greek island of Crete last Friday, the IOM said around 320 people remained missing, presumed drowned.
Rescuers pulled some 340 people to safety but there has been much uncertainty about how many people had been onboard the ship.
IOM said today that based on testimony from several survivors it was convinced there had been either 648 or 650 men, women and children onboard.
The survivors, spokesman Joel Millman said, "were sure of the number because smugglers counted them twice a day before departure".
The girl survived, but the rest of her family perished.