A total of 2,856 people were either dead or missing, IOM figures said.
In a previous update made on Tuesday, the IOM said that 206,400 migrants entered Europe by sea in 2016 as of June 5, with 2,809 fatalities recorded.
In the week spanning June 1-8, 1,514 people arrived, an almost 90 percent decrease from the week before, when 11,614 people arrived. Italy took the bulk of arrivals, with Greece and Bulgaria taking in 289 and 325 migrants respectively.
Europe has been beset by a massive refugee crisis, with hundreds of thousands of undocumented migrants fleeing their crisis-torn countries in the Middle East and North Africa to escape violence and poverty. The majority of them cross the Mediterranean Sea and arrive in the European Union using southern EU nations as transit points. More than 1.8 million refugees are estimated to have arrived in the European Union in 2015, according to the European border agency Frontex.