Bassie Mkhumbuzi was a member of the Azanian People's Liberation Army unit that killed 11 people and wounded 58 others in a automatic rifle and handgrenade attack on the church's congregants in Cape Town on July 25, 1993.
"Whites used churches to oppress blacks. They took our country using churches and bibles. We know and we have read from books they are the ones who have taken the land from us," Mkhumbuzi said.
Truth Commission lawyer Robin Brink said Mkumbuzi and his comrades perpetrated a "mindless barbarity" on defenceless people praying in a house of worship.
"Was it a revenge attack?" he asked Mkhumbuzi.
"No," Mkhumbuzi replied, "we just wanted our land to be brought back to us, not because we were revenging the actions of the church."
Mkhumbuzi, who was 17 years old at the time of the incident, said he had not been told beforehand by unit leader Sichumiso Nonxuba that a church was the target.
Nevertheless, "I felt that whites were using churches to oppress blacks".
There was confusion at the start of Wednesday's amnesty hearing in Cape Town when it emerged that one of the amnesty applicants - former Apla operations director Letlapa Mphahele - had failed to turn up.
The whereabouts of Mphahlele were not known, lawyer Norman Arendse told the amnesty committee chaired by Judge Hassen Mall.
Arendse said he represented Mphahlele's co-applicants Mkhumbuzi, Thobela Mlambisa and Gcinikhaya Makoma.
Makoma was found guilty on 11 counts of murder and 58 counts of attempted murder in March 1995 and sentenced to 23 years' imprisonment.
Mkhumbuzi, a member of the SA National Defence Force, and Mlambisa are on trial facing similar charges relating to the attack.
"We don't know where he (Mphahlele) is," Arendse said.
"He has not given us any instructions. We can't understand and we don't have any reasons why he is not here. We ask that his application be withdrawn at this stage."
Ian Bremridge, the lawyer for two of the victims opposing the amnesty applications, said Mphahlele's absence could be problematic as the other applicants intended testifying that he ordered the attack.
The applications are being opposed by Dawie Ackermann, whose wife was killed, Lorenzo Smith and Ukranian sailor Dmitry Makogon, who lost both legs and an arm in the incident.
Mkhumbuzi said while he sought forgiveness from the victims, "we could not stop what was happening at the time".
"We were fighting for our country and for democracy. It was difficult at the time to stop such incidents. The purpose of Apla at that time was to fight until the land was brought back to its owners."
Bremridge: "Do you thing the attack achieved anything?"
Mkhumbusi: "Yes. Today We are in this country. We are living together. We are not fighting together."
On the day of the attack he had remained in the getaway vehicle while Nonxuba - who was killed in a car accident last Novemmber - and Makoma entered the church armed with R4 rifles and M26 handgrenades, which he had fetched earlier from Apla high command in Umtata.
"I was told that I would be the security, Mlambisa the driver. Nonxuba and Makoma were going inside. After they came out of the building, I was to use the petrol bombs to throw them inside.
"I heard a grenade and gunshots and then saw a red car stopping in front of us, apparently to block us.
"I got out of the car and threw a petrol bomb at the car and Mlambisa shot at the car causing it to speed away."
He said it was only later that night, while watching a television broadcast by CNN, that he saw for the first time what had happened inside the church.
Mlambisa testified later that he was an Apla unit commissar based in Transkei when he was ordered to travel to Cape Town to take part in the operation.
He only realised the target was a church when the team drove up to the target in Kenilworth, Cape Town.
"I deeply regret the loss of lives and causing so many people to be injured," he said.
The hearing is set to continue on Thursday.