"The survivors, including a girl in critical condition, are suffering from hypothermia and were hospitalised in Chania on the island of Crete", a spokesman said on Saturday.
Two cargo ships, one flying the British flag and one from Libya, alerted Greek authorities after pulling seven people and a body from the wreck in the waters near the island of Malta.
A young girl later died from her injuries and the two bodies are still on the boats. Maltese authorities have opened an inquiry into the accident.
This year has seen a surge in the numbers of migrants attempting to make the hazardous crossing from north Africa and the Middle East to Europe.
More than 100,000 have reached Italy since the turn of the year and nearly 2,000 have perished in the attempt, according to the UN refugee body UNHCR.
Athens this month asked Brussels for an extra 63 million euros ($83 million) in EU funds to cope with the "dramatic" rise, which they predict could see migrant numbers triple this year.
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