Hasanuddin, still on trial for the crime, pleaded for forgiveness from the parents of the victims during the meeting, organised by local police. He said repeatedly that he had repented and expressed his deep sorrow together with his two accomplices, Irwanto and Haris.
A mother of one of the victims said with tears that she forgave them of their wrongdoings. As a gesture of peace, the Muslim militants and the Christian families shook hands and embraced each other, Asia News has reported.
The police chief, Sutanto, commented that the meeting between the two parties was a historic moment, giving the victims' families and the murderers the opportunity to "exchange their deepest feelings and seek to forgive".
The Vice President of Indonesia, Jusuf Kalla, hoped that this meeting would open a door to peace in Poso.
Hasanuddin, Irwanto and Haris have pleaded guilty to the charges of killing the three girls. They could face a death sentence if convicted.
The victims, Theresia Morangke, 15, Alfita Poliwo, 17, and Yarni Sambue, 15, were ambushed and beheaded on the way to their private Christian school in October 2005.
Poso is located in the central Sulawesi, which is about 1,000 miles northeast of the Indonesian capital Jakarta.