Another worker was accused of kidnapping, molesting and raping the same boy.

The ACT Human Rights Commission recently conducted an investigation into the allegations after receiving complaints from the child's mother.

Other allegations included that another youth worker threatened to have children arrested and about 47 carers rotated through the boy's placement within six months.

Children and young people commissioner Alasdair Roy was asked to investigate the accusations, which relate to the actions of three employees who worked for an agency that provided care services early last year.

Mr Roy could not conclude on the molestation complaint because the incident had been referred to police.

Michael David Watt, 25, was last year charged with child sex offences in relation to the allegations.

The mother alleged Watt once kidnapped her son for six hours, and taught him to masturbate and kiss.

Watt died before the court proceedings were finalised.

The organisation's name was suppressed by the ACT Magistrates Court.

Mr Roy's report revealed the organisation conducted an investigation into the throat grabbing claim after the boy complained to other staff members.

The allegation was unsubstantiated but the organisation transferred the accused youth worker to another unit.

The organisation also found the threats of arrest were not proven, but an email from the area manager had flagged concerns about strategies used by the employee.

The staff member was provided with support and advice on how to improve her communication with children.

The watchdog closed the investigation in August after making recommendations for the organisation to strengthen its policies and procedures for staff dealing with children in care.

Mr Roy's administrative inquiry is the second to be conducted into the organisation.

The ACT government conducted a review into how the accused child molester gained access to his alleged victim, despite being the subject of similar allegations in New Zealand.

Watt was charged with seven offences - including sexual intercourse and committing acts of indecency on a child - after he allegedly molested a 12-year-old boy.

Watt was found dead at his Conder home in May last year, less than a month after he was released on bail, and days before his next court date. He had no criminal convictions and had not entered pleas to any of the charges.

The Community Services Directorate confirmed an audit of the organisation had been conducted, but the findings would not be made public. "As this report is audit and commercial in confidence and part of an internal quality improvement program, it is unsuitable to be publicly released," a spokesman said.

Mr Roy also sought, and was refused, access to the document in the course of his inquiry.