"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.
These boats would typically have been carrying 120-140 migrants each, she added.
Lanuza said the bodies recovered were African men with estimated ages of between 16 and 25.
They had drowned, apparently in the 24 hours prior to being discovered early on Thursday morning.
Despite rough winter seas, migrant departures from Libya on boats chartered by people traffickers have accelerated in recent months.
Over 5,000 people have been picked up by rescue boats since Sunday, bringing the number brought to Italy since the start of 2017 to over 21,000, a sharp rise on the same period in previous years.
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