Its Algerian chairman Mohamed Bedjaoui, Francoise Kayiramirwa from Burundi and Pramila Patten from Mauritius were welcomed in the capital Conakry by Justice Minister Siba Lohalamou.
The trio, who will be in Guinea until 4 December, will on Thursday meet Guinean junta leader Captain Moussa Dadis Camara, Prime Minister Kabine Komara and other members of the junta that seized power last year.
As the investigators arrived, the United Nations urged Guinea's leaders to stick to their promise of working with the commission.
"Captain Camara and the members of the government have said very clearly that they would cooperate fully," Said Djinnit, special representative of UN Secretary General Ban Ki-moon in west Africa, told AFP and RFI radio.
The commission of inquiry was approved in October by the UN Security Council. Its secretariat arrived in Conakry on 15 November.
Scores of demonstrators were killed in Conakry's biggest stadium on September 28 as they gathered to protest Camara's plans to run in a presidential election he had slated for January.
The military junta said 56 people were killed and 934 were injured. Human Rights Watch said the attack on the protesters was organised and premeditated, and put the death toll at 157. The United Nations believes 150 were killed.
Camara came to power in a bloodless coup on December 23 after the death of dictator Lansana Conte, who had led the country since 1984.
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