"As Apla we are going to apply for amnesty so that those innocent ANC people convicted of the crime can be freed," Mphahlele told Sapa.
The murders of Sandra Mitchley, her son Shaun Nel and friend Claire Silberbauer at Eikenhof in March 1993 made national headlines as did the subsequent arrests of Boy Ndweni, 19, Siphiwe Bholo, 24, and Sipho Gavin, 22.
The three, who told the court they were ANC Youth League members, were accused of ambushing and killing Mitchley and the children on the Vereeniging highway south of Johannesburg.
After the attack, a man purporting to be an Apla spokesman telephoned the South African Press Association to claim responsibility for the ambush.
However, the possibility of Apla's involvement was ignored after police announced the arrest of two ANC members.
Then Law and Order Minister Hernus Kriel congratulated the police at the time on their excellent detective work in arresting the suspects.
On Thursday, Mphahlele also revealed that he and Maj Thembelani Xundu, a former Apla cadre, would seek amnesty for the 1992 attack on the King William's Town golf club in which four people were killed and 17 injured.
Xundu, who was integrated into the SA National Defence Force and is now based in Umtata, is presently on trial in the King William's Town magistrates court. He is due to appear again on March 20.
Mphahlele said Xundu had decided to apply for amnesty - he initially said he had no intention of doing so - after a recent meeting of Apla's high command.
"They felt that there was no use in not taking part in the amnesty process when we have hundreds of members in prison.
He said four Apla members, including himself, would seek amnesty for the July 1993 St James Church massacre in Kenilworth, Cape Town in which 11 people were killed and 56 injured.
He identified a second applicant as Gcinikhaya Makoma, who is serving a 23 year jail sentence for his part in the attack.
Mphahlele also said he intended meeting survivors of the King William's Town golf club and St James attacks for "a heart-to-heart encounter" in the spirit of national reconciliation.
He was also trying to meet the victims of other Apla attacks in the Free State.
As former operations director he would accept responsibility for all Apla operations which took place between 1990 and 1994.
Although few amnesty applications had been sent to the Truth Commission so far the PAC expected to submit about 600 including 500 from prisoners, before the May 10 deadline.
The entire Apla high command - numbering about 40 people - intended seeking amnesty, he said.
Former Apla commander Brig Dan Mofokeng, now chief of staff at Natal Command, had already submitted an application.
Applications were still to be made by Brig Mosuoe Magalefa, now based at army headquarters in Pretoria, and PAC MPL Joe Mkhwanazi, a member of the KwaZulu-Natal provincial legislature.
Mphahlele said Apla was planning to hand over 300 applications to the Truth Commission "as a sign of good faith" at a meeting before the end of the month.
At the meeting, a date for which has not yet been set, the PAC would also highlight the plight of its members in prisons.
Many had been targeted for beatings by white warders and intimidation and assault by prison gangs.
In the interim, Apla's high command was still busy compiling a submission which would detail specific military operations in South Africa and name, for the first time, at least 10 people who were executed in exile on suspicion of being South African agents.
The names, death certificates and burial site numbers of members who died of natural causes in Lesotho, Mozambique, Zambia and Tanzanian would also be released.