"When we should have been comforting and praying for those in desperate need we sometimes joined the cheering crowds and urged on the gladiators...," he said.
McCauley, who is also head of the Rhema Church, was testifying in East London on the third day of the Truth and Reconciliation Commission's special hearing into the role of the church under apartheid.
He said the IFCC was formed in 1984 and consisted of about 400 member churches countrywide.
"Paralysed by a false respect for government authority, most of our white charismatic and Pentecostal church followers were simply spectators to the horrible acts of abuse of humanity in this country," he told a panel chaired by TRC head Archbishop Desmond Tutu.
"We must confess that many of us allowed ourselves to be swayed and manipulated by a government propaganda machine that tried to portray freedom fighters as the enemies of the church and of Christianity in particular."
He admitted that black members of his church were ostracised and rebuked when they spoke out against apartheid.
"We, the white members of the leadership of our charismatic and Pentecostal churches, seek the forgiveness of our black counterparts in the church.
"We seek the forgiveness of colleagues within the larger religious community for the times when we lacked the courage and conviction to walk alongside you in your demands for justice and righteousness."
The tragedy of the "sometimes callous" attitude of hundreds of thousands of Christians in South Africa would forever stain the history of Christianity in South Africa.
"The guilt of many South African Christians is even greater because the laws of apartheid and the subsequent abuse of power by a security system and police force, that at times seemed to come from the pit of hell, was aimed at fellow Christians.
"We know that many Christians within our constituency, still to this day, find it hard to accept any responsibility for what happened in the past."
While many were prepared to admit that apartheid was a mistake, they were only willing to offer a half-hearted apology.
"That sort of confession, in my mind, is cheap and fails to get to grips with true confession which leads to repentance, that in turn leads to meaningful forgiveness, followed by restitution and reconciliation."
McCauley also said the churches needed to play a more active role in redressing past econcomic imbalances.
"The issue of land acquisition is key to giving people a sense of dignity and belonging, and my sincere prayer is that those church organisations that hold unused property will generously show the hand of true Christian charity."