The man, who cannot be identified, was arrested in Adelaide on Thursday and charged with offences that allegedly occurred at the Magill Youth Training Centre between 1978 and 2003.
The male-only detention centre in Adelaide's east was closed in the early 2010s.
The arrested man, 73, appeared in Adelaide Magistrates Court, where prosecutors opposed all forms of bail.
He faces 55 charges including multiple counts of rape, unlawful sexual intercourse, sexual abuse of a child, gross indecency and indecent assault, involving 29 alleged victims.
The charges relate to 29 victim-survivors, many of whom were children when the offences were allegedly committed.
A prosecutor told magistrate Patrick Hill the defendant had escaped detection for many years "through intimidation and violence towards complainants and through ingratiating himself into Aboriginal community groups".
Police have spoken to a further 19 complainants who had alleged sexual abuse, but had expressed "some reticence about providing witness statements", she said.
Including those allegations, the timeframe of the alleged abuse spanned 1971 to 2005.
"They're engaging with police, but there is a risk that those witnesses will be deterred from engaging with police if the defendant remains in the community," the prosecutor said.
A majority of the complainants were Aboriginal children who came into contact with the accused man at difficult times in their lives when they did not have anywhere to live or were themselves in custody.
The prosecution's cases would depend on ongoing witness cooperation.
The man's identity and occupation were suppressed.
A duty solicitor told the court the man had suffered a stroke and also had a "significant brain injury" that would "make him more vulnerable than the average person that comes before the court".
The magistrate remanded the accused rapist in custody pending a home detention report being presented to the court on September 18.
He will face a charge determination hearing on January 12.
Police Assistant Commissioner Stuart McLean said detectives under the banner of Task Force Libero had scrutinised allegations of historical child sexual abuse at Magill and other government care facilities.
"Today is the first arrest for Libero," he said.
"I anticipate potentially further arrests as these investigations continue."
There were previous historical allegations of sexual abuse at the centre, which was criticised for its poor conditions before its closure in 2012.
Mr McLean said he was very proud of the detectives' complex and protracted investigation, which began in December 2023 before the taskforce was formed in March 2025.
"They work with victim survivors of these offences, and they're complex matters that take significant investigative effort," he said.
"And when we have sufficient evidence to support laying a charge, we will do so and bring people before the court."
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