"Despite deteriorating weather conditions, approximately 48,000 refugees and migrants crossed from Turkey to the Greek islands, or about 9,600 migrants and refugees in each of the past five days," the IOM said in a statement, referring to the period between October 17 and 21.
The number of arrivals peaked on Tuesday when nearly 11,000 people had landed on the Greek islands, the organisation said.
"The influx has left many local authorities unprepared," the IOM said.
More than half of those crossing from Turkey had landed on the island of Lesbos, which saw 27,276 arrivals during the five-day period, it said.
The island of Chios recorded 9,750 arrivals over the same period.
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In previous years, the numbers crossing the Mediterranean to Europe have dropped off sharply as winter approaches, but the IOM said the recent arrivals far exceeded the summer peaks.
Chios, which had only been receiving some 300 migrants a day during the peak summer period, was last week taking in around 2,000 a day, it said.
They are among more than 600,000 people, mainly fleeing violence in Syria, Iraq and Afghanistan, who have braved the dangerous sea journey to Europe so far this year.
The rising numbers of people attempting the crossing to Greece has resulted in a growing number of deaths at sea, the organisation said.
Since Monday, 18 migrants and refugees are believed to have died in two separate incidents.
So far this year, around 335 people have died while crossing from Turkey to Greece, the IOM said.
More than 2,800 have meanwhile perished attempting the much longer and more perilous crossing from Libya to Italy, bringing the total number of deaths to 3,175, the IOM said.