IOM's announcement came just a month after the 100,000-mark was passed, and the United Nations warned the surge in arrivals was creating humanitarian crises that required a "collective and far-reaching" European response.
Nearly all of the people who have crossed the Mediterranean so far this year have landed in Italy, which has counted around 75,000 arrivals, and Greece, which has seen the numbers explode.
So far this year, more than 77,000 people have landed on Greek shores, compared to only 34,442 for all of 2014, according to the UN refugee agency, which on Friday warned the country was facing a "growing humanitarian crisis".
"On average, 1,000 arrive every day on the Greek islands," UNHCR spokesman William Spindler told reporters in Geneva, adding that most of them were fleeing from war-ravaged Syria.
"The numbers of people arriving are now so high that despite all efforts, the authorities and local communities can no longer cope," he warned, insisting "urgent response from Europe is needed before the situation deteriorates further."
"Greece urgently needs help and we expect Europe to step forward," he said.
EU leaders agreed last month to redistribute 40,000 Syrian and Eritrean asylum-seekers already in Europe to help take the load off countries like Greece and Italy, but on a voluntary basis after many member states objected strongly to proposed mandatory quotas.
The crisis is being felt further afield as well.
Nearly all of the migrants and refugees who arrive in Greece, where the reception capacity is "completely overwhelmed", move on, trying to reach western and northern Europe by passing through the western Balkans region.
Spindler said that in June, the number of people crossing from Greece into Macedonia and Serbia had soared to an average of 1,000 per day.
"The capacity of these countries to effectively respond to the emergency situation is severely overstretched," he said, insisting though that "the tightening of borders and building of walls (as Hungary is planning to do) are not the solution."
"We would expect the European Union to activate its emergency response, because Greece is part of the European Union, and this is happening in Europe.
"It is happening on the doorstep of Europe," Spindler said, also demanding more assistance to countries in the "immediate EU neighbourhood" like Macedonia and Serbia.
As Europe grapples with how to handle the massive numbers who make it to its shores, IOM pointed out that 1,914 people had died trying to cross the Mediterranean this year — more than twice as high as at the same point in 2014.