OIM spokesperson Flavio Di Giacomo said it was still investigating whether some migrants on the boats had already been rescued by the Libyan coastguard.
Five bodies have been pulled from the sea but aid workers believe there were at least a total of 240 migrants on both boats.
"We don't think there can be any other explanation than that these dinghies would have been full of people", said the charity's spokesperson Laura Lanuza. She added that the inflatables, of a kind usually used by people traffickers, would typically have been carrying 120-140 migrants each.
The UNHCR cited NGO sources saying the five bodies were recovered about 14 miles off the Libyan coast near two empty and partially submerged rubber dinghies.
The U.N. refugee agency said it was "deeply alarmed" by the reports.
The UNHCR said the latest incidents come after an intense week of arrivals through the central Mediterranean route with nearly 6,000 migrants and refugees rescued in five days this week.
More refugees died in the Mediterranean over the first nine weeks of 2017 compared with the same period in 2016, the International Organization for Migration (IOM) says.
Lanuza said the boats were found Thursday morning, north of the Libyan town of Sabratha.
Prior to the latest fatal incident, the United Nations had estimated that at least 440 migrants had died trying to make the crossing from Libya to Italy since the start of 2017.
Although 2016 was the deadliest year ever recorded on the Mediterranean - with 5,096 lives lost - there are fears that the 2017 death toll will rise even higher.
Last month, European leaders signed a controversial plan to help stem the flow of African migrants to Europe.
In a tweet, the group said: "There will be many more".
Information for this article was contributed by Aritz Parra, Maggie Michael and Christopher Torchia of The Associated Press.