Cyril Alfred Hughes was working as a teacher at Marist Brothers College in western Sydney when he allegedly molested the teenage boy between 1982 and 1985.
The 82-year-old was found mentally unfit to stand trial at Parramatta District Court on Tuesday because of a deterioration in a constellation of medical conditions including non-Hodgkin lymphoma, chronic back pain and kidney failure.
Under NSW law for those with significant mental impairments, Hughes was taken to have pleaded not guilty to two charges of indecent assault and two charges of homosexual intercourse between a teacher and student.
At the time of the allegations in 1985, the alleged victim - who cannot be legally named - was 16 or 17 years old.
Before a special hearing which is estimated to take four to six weeks, Hughes' barrister Bill Neild SC applied to the court for medical records from the complainant.
The documents were sought after the alleged victim spoke to a colleague and teacher last May about psychological treatment he had received at a hospital in Sydney's inner west.
During that session, he underwent a procedure known as eye movement desensitisation and reprocessing (EMDR) to gain a "flashback memory" of another alleged sexual assault by Hughes, the court was told.
Mr Neild said his expert would give evidence at the hearing about how EMDR could potentially affect a person's memory, impacting their reliability and credibility.
The alleged victim's Legal Aid solicitor Edwin Hulme opposed the documents being released, saying this could harm his client.
Hughes' legal team had other material it could use to back its case that EMDR produced "affected memories," Mr Hulme argued.
At the time the alleged victim underwent this procedure, he was under a high degree of stress because the criminal case had stretched on for five years, he said.
Judge Karen Robinson ordered the medical records be handed over.
She said the documents had substantial probative value as they could show whether any treatment received impacted the complainant's memory.
However, to protect the alleged victim, the judge said the documents would be given to the court with Mr Hulme able to eyeball them first before they were released to Hughes' defence team.
The matter will return to court for further preliminary arguments before the special hearing begins.
1800 RESPECT (1800 737 732)
National Sexual Abuse and Redress Support Service 1800 211 028