Allan Keith Huggins is accused of molesting 13 vulnerable teenage boys in Sydney and the rural NSW town of Armidale from 1977 to 1986.
He is alleged to have either sexually touched or raped the teens at a youth centre for troubled boys, as well as at a school and his private practices.
Police and a local bishop did not believe two of the alleged victims when they came forward to make their complaints, Sydney's Downing Centre District Court previously was told.
The trial continued on Tuesday, when jurors heard two Armidale children were referred to Huggins by court and state officials before they were allegedly abused.
Crown prosecutor David Patch said a nine-year-old boy was referred to the counsellor in the 1980s after his mother contacted NSW departmental officials.
The boy was allegedly sexually touched and masturbated by Huggins.
On one occasion, the youth also believed the counsellor masturbated behind him as he faced a wall in the clinic, Mr Patch said.
Although the alleged victim approached police and made a statement in 1990, that document had disappeared and nobody knew where it had gone, the jury was told.
Another alleged victim, who now identifies as a woman, was over 16-years-old when she was referred to Huggins after coming before a children's court magistrate.
Mr Patch said the counsellor used his authority to force the teen into sexual activity.
"You need a good report for the courts; just relax, you're alright," he allegedly told the teenager.
On one occasion he sucked the teen's genitals, to which she said "stop, stop" while the alleged assault continued, the jury heard.
After that, the counsellor again tried to exert his influence, the prosecutor said.
"If you tell your mum, she won't believe you," the counsellor allegedly said.Â
The teen and Huggins later had consensual sex, but on one occasion he was too aggressive, Mr Patch said.
She had to get new clothes as her pants were left full of faeces and blood, the court heard.
She buried the underwear she was wearing at the time under her home in a plastic bag, which was recovered by police in 2014.
Huggins, who is now in his 70s, has pleaded not guilty to 42 charges, including indecent assault, sexual assault and sexual intercourse without consent.
Other allegations against him include that he fondled the genitals of two brothers after they appeared in his private practice.
Another boy was summoned to Huggins' office at school, where he was allegedly raped despite making a noise due to the pain, the jury heard.
"The accused covered his mouth with his hands so (the boy) had trouble breathing," Mr Patch said.
Jurors previously heard Huggins groomed his alleged victims through "relaxation" techniques that involved the teens stripping down and being touched.
In the 1990s, the counsellor relocated to Western Australia, where he worked with the state government to find employment for homeless and vulnerable teens.
He was charged and pleaded guilty to one count of indecent dealing when he massaged and inappropriately touched a 15-year-old boy in an Albany hotel room, the court was told.
Huggins' barrister, Roland Keller, did not make opening submissions.
The trial before Judge Penelope Hock continues.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028
