"The recent spate of Mediterranean Sea tragedies along all three migratory routes have brought the number of confirmed fatalities in 2019 to 994 men, women and children," the agency said in a statement.
The IOM added that it was still trying to confirm reports of as many as 40 migrants who were lost in a shipwreck off Morocco's coast during the weekend.
This marks the sixth consecutive year that over 1,000 people will have been reported killed in the waters of the Mediterranean, the IOM added, with a total of at least 15,000 people having been killed during that period.
On 18 September, the agency said that over 63,000 people had reached Europe by crossing the Mediterranean in 2019. This was a 20 percent decrease from the same period of the previous year.
Since 2015, Europe has been experiencing its worst migration crisis in recent history, struggling to accommodate hundreds of thousands of refugees and migrants fleeing hostilities in Middle Eastern and North African countries. However, over recent years the flow of migrants has been steadily going down due to various factors, including the winding down of the war in Syria and a number of European countries embracing a stricter border security and immigration policies.