Three people were left drifting by Libya's coast guard, the NGO said; only one survived.
An aid group has accused Libya's coast guard of abandoning a woman and a toddler to their deaths in the Mediterranean Sea after intercepting 160 Europe-bound migrants.
Proactiva Open Arms, a Spanish rescue group, said it found three people amid the drifting remains of a destroyed boat 80 nautical miles from the coast of the north African nation.
It said it found one woman alive and another dead, along with the body of a toddler.
The organization posted images and videos of the wreckage and the bodies on social media, accusing both a merchant ship sailing in international waters and Libya's coast guard for failing to help the three migrants.
Libyan Coast Guard spokesman Ayoub Gassim said earlier that a boat carrying 158 passengers, including 34 women and nine children, had been stopped Monday off the coast near the town of Khoms. He said the migrants were given humanitarian and medical aid and were taken to a refugee camp in Khoms.
Libya has emerged as a major transit point to Europe for those fleeing poverty and civil war in Africa and the Middle East. Traffickers have exploited Libya's chaos following the 2011 uprising that toppled and killed longtime ruler Moammar Gaddafi.
Europe's Border Crisis
Italy's new populist government has vowed to halt the influx of migrants across the Mediterranean and has given aid to Libyan authorities to do that. Human rights activists have sharply criticized that assistance, saying migrants being returned to Libya are at risk of facing beatings, abuse, rape and slavery.
The head of Proactiva Open Arms, Oscar Camps, on Tuesday blamed the Italian government's cooperation with Libyan authorities for the death of the woman and the toddler.
"This is the direct consequence of contracting armed militias to make the rest of Europe believe that Libya is a state, a government and a safe country," Camps said in a video posted on Twitter.
Camps said the two women and the toddler had refused to board the Libyan vessels with the rest of the intercepted migrants, and so the three were abandoned in the sea after the Libyan coast guard destroyed their boat.
He also said their deaths were the result of not allowing aid groups such as Proactiva to work in the Mediterranean. Some 1,443 people are dead or missing in the dangerous Mediterranean Sea route up to July 15 this year, according to the U.N. migration agency.
Both Italy and Malta have blocked aid groups from operating rescue boats, either by refusing them entry to their ports or by impounding their vessels and putting their crews under investigation.
Italy's hardline Interior Minister Matteo Salvini rejected any criticism of his country's stance on migration.
"Lies and insults from some foreign NGO confirm that we are right: Reducing the departures and disembarkations means reducing deaths and reducing the earnings of those who speculate on clandestine migration," Salvini said in a Facebook post.
The U.N. migration agency said the number of migrants and refugees reaching Spain by sea this year has overtaken those who have arrived in Italy.
The International Organization for Migration said Tuesday that Spain saw 18,016 migrants come in up to July 15, while 17,827 people landed in Italy during the same period.