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Two of his victims, Paul Klemick and Michael Haggie, agreed to go public about their experiences with Mr Thompson, amid suggestions he abused at least 16 boys from the school.
"I think he was a predator," Mr Haggie said. "He just preyed on young boys who were very innocent."
Mr Haggie said he was abused daily by Mr Thompson throughout his senior years at the school, beginning in 1971 when he was 15.
Both men said Mr Thompson targeted other boys too, and Mr Klemick said he was once forced to perform sex acts on another boy while Mr Thompson watched.
And, when Mr Klemick finally confronted Mr Thompson, the teacher, fearing his secret would be revealed, took his own life, Mr Klemick said.
The school - which has since been replaced by the Catholic co-educational Kavanagh College - was at the time run by the Christian Brothers, a Catholic religious order.
The Christian Brothers had employed Mr Thompson after he was forced out of a Marist Fathers seminary in the North Island, allegedly after affairs with other seminarians, a third pupil said.
But, in the days following his death on January 15, 1985, staff at the school were told to keep quiet about any suggestion of suicide.
A former St Paul's staff member, speaking on condition of anonymity, told ODT Insight there had been "considerable" unease among staff about the behaviour of Mr Thompson and the nature of his death.
"I was there when the principal told all staff to say that the death was not a suicide," the former teacher said.
Instead, Mr Thompson's death was presented as a heart attack at the time, and he was farewelled at a big funeral at St Joseph's Cathedral, the victims said.
A brief coroner's report from June 1985, obtained by ODT Insight yesterday, confirmed Mr Thompson's death was self-inflicted.
Mr Haggie believed some of the Christian Brothers at the school suspected Mr Thompson, "but they never came up with an accusation".
That left Mr Thompson free to behave as if it was "open season".
"He just saw he could get away with whatever."
Mr Klemick said Mr Thompson also kept nude photographs of his victims in a box at his home, including some of Mr Klemick.
But, when Mr Klemick let himself in after learning of Mr Thompson's death, he found the pictures were gone and the rest of the house was uncharacteristically tidy.
When he relayed his concerns to another teacher at the school, he was told not to say anything to police, he said.
Mr Haggie said events took another turn when it later emerged Mr Thompson had left his home and possessions to another former pupil from the school.
The school and the Christian Brothers order which founded it were already in the spotlight after ODT Insight last month revealed more details of offending in Dunedin.
That included the activities of the paedophile priest Fr Magnus Murray and fresh allegations of abuse against Br Desmond Fay and a second Christian Brother, who cannot yet be named.
All three men were employed by the Christian Brothers to teach either at St Paul's or the Christian Brothers Junior School in the 1960s or 1970s, before Mr Thompson joined St Paul's.
The St Paul's principal at the time, Br Tony Gherardi, has since died, and St Paul's was replaced by another Catholic school, Kavanagh College, in 1989.
Dunedin Bishop the Most Rev Michael Dooley told ODT Insight the diocese had no record of complaints relating to Mr Thompson, but he was "shocked and deeply saddened" by the allegations.
The school's board of governors was responsible for employing Mr Thompson, but the alleged offences should be investigated, Bishop Dooley said.
That could be done by the police, the church's National Office for Professional Standards or as part of a pending Royal Commission into historic abuse, he said.
Kavanagh College principal Tracy O'Brien said he had not been approached by anyone with allegations of historic offending by Mr Thompson, or anyone else at St Paul's High School.
"To the best of my knowledge neither has any staff or board member during my tenure," he said.
Mr O'Brien said he supported Bishop Dooley's recent public apology for the impact of historic sexual abuse and the church's handling of it, and would "continue to look to the bishop's leadership on any historical matters".
A New Zealand Police spokeswoman declined to comment, and the Government is yet to confirm the scope of its Royal Commission.