Among churches making submissions at the special three-day hearing in East London was the Anglican Church, which tendered a particular apology to TRC chairman Archbishop Desmond Tutu, who recently retired as its spiritual leader.
The church - officially known as the Church of the Province of Southern Africa - apologised for its failture to support him in the face of harsh criticism over his call for economic sanctions on South Africa in the 1980s.
Joining the church at Monday's hearing were representatives of the Catholic, Presbyterian, Congregational, Methodist and Reformed Presbyterian churches as well as the SA Council of Churches and the evangelical Church of England.
Their submissions were heard by a panel chaired by Tutu, who began by telling the churches that none of them could claim a perfect record in opposing apartheid.
"We are here to say to God, and the world, that we have fallen short of your glory. There is no church I know of that will not have something to confess to shortcomings."
In a submission praised by the TRC panel, Bishop Michael Nuttall admitted the Anglican church had been complacent in challenging apartheid policies.
"The CPSA acknowledges that there were occasions when, through the silence of its leadership or its parishes, or their actions in acquiescing with apartheid laws where they believed it to be in the interests of the church, deep wrong was done to those who bore the brunt of the onslaught of apartheid."
This moral lethargy had been bolstered in part by the fact that the church had, over the years, developed its own pattern of racial inequality and discrimination.
"It was all too easy to pass resolutions or make lofty pronouncements condemning apartheid. It was all too easy to point a morally superior finger at Afrikaner nationalist prejudice and pride.
White Anglicans owed the Afrikaner community an apology for their attitude of moral superiority, Nuttall said. However, the church's chief apology had to be to its black congregants, who comprised the overwhelming majority of its members.
White parishes had, like white business, benefited from apartheid.
In tendering the church's apology to Tutu, Nuttall described the Nobel Peace Prize winner's call for economic sanctions as a single-handed act of moral courage.
"It could be said... that we took too long... we allowed others to precede us and take the flak."
The evangelical Church of England said it allowed itself to be misled by the former National Party government into accepting a cruel and oppressive system.
Bishop Frank Retief said the government used the Bible to support its policies and to give the impression it was a Christian government.
"Many members of the Church of England in South Africa generally and honestly believed the government's propaganda about the communist threat," Retief said.
"Be that as it may, the fact of the matter is that we allowed ourselves to be misled into accepting a social, economic and political system that was cruel and oppressive."
The church's insistence on remaining a neutral party in the apartheid conflict was, in hindsight, a major error.
"We declared ourselves to be apolitical, and in this way failed to adequately understand the suffering of our many black members who were victims of apartheid.
The Catholic Church's record as a staunch opponent and vocal critic of apartheid was sketched by Bishop Kevin Dowling, who told of the church's teachings condemning the system, its financial support for the alternative newspaper New Nation, and its role in helping to establish a culture of human rights.
"The complicity of the Catholic Church in the past is found in acts of omission rather than comission," Dowling said.
"There were times... when it was more concerned with itself as an institution, rather than as a servant of God's people, times when it was more concerned with not having expatriates deported than with drawing attention to the wrongs being done.
"Silence in the face of ongoing and systematic oppression at all levels of society is perhaps the church's greatest sin."
The church's submission was also critical of the "expedient" political settlement that gave rise to the TRC.
"From the inception of the TRC we were dissatsifeid that victims/survivors were asked to sacrifice individual justice for the truth."
In another submission, the Institute for Contextual Theology proposed a separate TRC to probe the role of churches under apartheid.
The present truth and reconciliation process was limited because it was the product of a political settlement, the institute said.
General-secretary Wesley Mabuza proposed that a special wealth tax be levied on people who benefited economically, whether directly or indirectly, from apartheid.
The SA Council of Churches admitted churches made little concerted effort to stand together against the former regime.
SACC general secretary Dr Brigalia Bam said the council played a key role in the struggle against apartheid, but failed to be more proactive in its opposition to the government's policies.