The Geneva-based intergovernmental organization said on Tuesday that the million mark was crossed on December 21. The huge milestone is a more than a four-fold increase on last year's figures.
IOM said more than 800,000 crossed into Greece from Turkey, including more than 455,000 from Syria and over 186,000 from Afghanistan.
Out of a total of 1,005,504 arrivals by December 21, the vast majority - 816,752 - arrived by sea in Greece, IOM said. Almost 3,700 people died as they tried to make the perilous journey across the Mediterranean.
IOM chief William Lacy Swing said in a statement on Tuesday that it "wasn't enough" to count the numbers.
"We must also act. Migration must be legal, safe and secure for all - both the migrants themselves, and the countries that will become their new home," said Swing.
Looking ahead to 2016, the United Nations refugee agency, UNCHR, expect the arrival rate to be similar to this year. IOM spokesman Joel Millman said it was impossible to forecast future numbers, however.
"So much is in the balance, the resolution of the Syrian war, and the disposition of the European border protection moves that are being contemplated," Millman said.
"We never thought it would reach this level. We just hope people are treated with dignity."
Europe is currently facing its biggest wave of mass migration since the Second World War. The next challenge facing European leaders is the redistribution of the hundreds of thousands of asylum seekers across the continent.
So far this year, only 1 percent of asylum seekers have been relocated and hardly any have been accepted by eastern European countries such as Poland, Hungary, the Czech Republic or Slovakia.
Earlier this year Slovenia, Hungary, Austria and Macedonia all erected fences to stem the flow of asylum seekers to their country.
German Foreign Minister Frank-Walter Steinmeier warned eastern European nations on Saturday, however, that by refusing to accept refugees, they risk facing funding cuts and legal sanctions.
ksb/jil (AP, Reuters)