Proactiva Open Arms spokeswoman Laura Lanuza said their vessel was heading north to the Italian port of Catania to hand over the bodies of the five young men found yesterday.
She said that other NGOs are continuing the search for possible victims off Libya's coast.
The UN refugee agency said it was "deeply alarmed" by the reports. Both it and Proactiva said they feared the death toll may be much higher as migrant dinghies are normally crammed with around 120 people each.
Lanuza said the boats were found yesterday morning, north of the Libyan town of Sabratha. The five men of African origin were estimated to be between 16 and 25 years old and appeared to have drowned, she said.
The Red Crescent in Libya, and the Libyan coast guard, said today that they had no reports about dead migrants or capsized boats in the 20 kilometers of Libyan territorial waters.
It said so far this year some 21,903 people had crossed the Mediterranean Sea to European shores.
The agency said that since the beginning of 2017, and excluding the latest incidents, around 590 people have died or have gone missing in crossings.
Last year was the deadliest ever recorded with 5,096 migrants perishing or going missing, according to the UNHCR.
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