Human Rights Watch and TRIAL International said they interviewed 30 former Gambian officials, including 11 officers, and a survivor of the round-up as part of a joint investigation.
The migrants -- 44 Ghanaians and several Nigerians, Senegalese, as well as a Togolese -- were arrested on a beach in Gambia while trying to reach Europe, suspected of being mercenaries wanting to overthrow Jammeh.
According to a joint statement by the NGOs, they were detained in the capital Banjul and handed over in groups to the "Junglers", a notorious paramilitary unit, and executed.
"Jammeh's subordinates then destroyed key evidence to prevent international investigators from learning the truth."
A joint report by the Economic Community of West African States and the UN, which was not made public, concluded in 2009 that the killings and disappearances were carried out by rogue members within the Gambian security services, with no credible evidence to suggest they were acting on orders from superiors.
"The new evidence makes clear, however, that those responsible for the killings were the Junglers," HRW and TRIAL said in their statement today.
In the statement, Martin Kyere, the only known Ghanaian survivor, told how his group was tied up in the back of a pick-up truck.
"It was then that I thought, 'We're going to die," he said.
But he managed to get free and escape into the forest, and later helped Ghanaian authorities identify many of the victims.
He fled the country the following month for Equatorial Guinea, where he finally conceded and handed over power.
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