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With just days left in 2015, the Geneva-based intergovernmental organization said 1,005,504 people had entered Europe as of Monday, more than four times as many as last year. Almost all came by sea, while 3,692 others drowned trying to make the crossing.
IOM director-general William Lacy Swing urged European governments to make migration safer.
"We know migration is inevitable. It's necessary and it's desirable," he said, adding: "Migration must be legal, safe and secure for all -- both for the migrants themselves and the countries that will become their new home."
The IOM compiles the numbers from government records in Greece, Italy, Bulgaria, Spain, Malta and Cyprus, spokesman Joel Millman said. He noted that the real number of people entering Europe may be even larger, because authorities are struggling to track all arrivals given the sheer volume.
Most of the people entered Europe via Greece, which took in more than 820,000 people this year, nearly all of them crossing from Turkey by boat across the Aegean Sea. Another 150,000 came into Italy across the Mediterranean from north Africa while smaller numbers crossed from Turkey by land into neighboring Greece and Bulgaria. Much smaller numbers arrived by boat to other Mediterranean countries.
Others -- not accounted for in the IOM tally -- crossed into Europe across other borders, such as a route from Russia to Norway where a few thousand people have crossed by bicycle.
About half of the people entering Europe were Syrians, while 20 per cent were Afghans and 7 per cent Iraqis, IOM said.
Of the deaths, 2,889 were people traveling from north Africa to Italy, the IOM said, 706 drowned trying to cross the Aegean to Greece and 72 died trying to reach Spain.
The war in Syria was particularly key in driving the numbers of people moving into Europe to levels not seen in half a century. European governments have struggled to agree on a response, arguing about how welcoming they should be and how best to manage the flows.
Over the summer, eastern European countries in particular opened and closed their borders, leading to widespread confusion and frustration, before a relatively orderly system emerged in the fall.
Germany and Sweden have welcomed the largest numbers of refugees. Germany has seen around 1 million migrants arrive this year, but that figure includes large numbers of people from eastern European countries.
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