The PAC's provincial secretary for information, Bonginkosi Njoli, said on Tuesday that Mbeki, as a senior African National Congress member, was supposed to know about the murders and should have mentioned them in his submission to the Truth and Reconciliation Commission.
He said members of the ANC's armed wing Umkhonto weSizwe (MK) who had been arrested in connection with the murders "operated under military commands".
Njoli was reacting to media reports about six MK members arrested in Port St Johns in connection with the murder of the five Apla members.
According to the police the men were killed execution-style after accepting a lift to Port St Johns in the former Transkei.
"It is most saddening to hear that MK members have been arrested in connection with the cold blooded murder of our comrades," Njoli said.
"The death of these Apla members was clearly well planned with a particular purpose of undermining our role in the struggle," he said.
Njoli extended his organisation's condolences to the families of the dead men, adding that the PAC would do its best to see that justice was done and that the deceased were reburied as true freedom fighters.
Meanwhile, Siyabulela Ernest Duba of Phakamisa township, a family member of one the slain Apla members, has accused the PAC of earlier failing to assist them when they inquired about the whereabouts of the men.
Duba said his younger borther, Falithenjwa Rasta Nkanyezi, left Beaufort West in 1994 to go to the Transkei to attend the funeral of Sabelo Phama. He was never seen alive again.
He said he asked other Apla members about his brother, but claimed they did not take the matter seriously.
"The PAC never came to our assistance when we approached them to inquire about the whereabouts of my brother," he said. "We hoped they would give us all the necessary assistance, but we left barehanded. They even told us that they knew nothing about the matter."
Duba said they first heard about his brother's death on television.
The family would like to know the reasons behind the death of the five men, he said, adding it was strange that the suspects were MK members, because Apla and MK had fought for the same cause.