Maree Welch raised suspicions that her daughter Bobbie had been abused by a casual worker at the Family Support Group (FSG)  in 1995 but will tell the commission that her complaint was not appropriately handled.

In the opening address of a public inquiry into disability organisations, the Royal Commission into Institutional Responses to Child Sexual Abuse heard Ms Welch told FSG co-ordinator Melissa Edwards she believed Bobbie may have been raped.

"I hate to tell you this, I think Bobbie has been interfered with, sexually molested or possibly raped – but I don't know whether it has gone as far as rape,"  the commission heard.

Ms Welch, who is due to give evidence, will tell the inquiry she was later threatened with legal action.

"FSG's solicitor wrote to the Welches. The letter asked the Welches to cease and desist making defamatory statements about FSG," counsel assisting the commission Gail Furness said.

The inquiry will hear evidence about two other providers, the Mater Dei School in Camden and the Disability Trust, south of Sydney.

The commission was told a former teacher at the Mater Dei School left Australia after being suspected of abusing three children with disabilities at the facility in the early 1990s. Chief executive and principal of the school Tony Fitzgerald has been called to give evidence.

The inquiry will also hear evidence from a woman whose young son was allegedly molested by a staff member at the Disability Trust in 2012. The hearing was told police investigated the case but the alleged perpetrator was not charged as the young boy, who has autism, was unable to give evidence in court. Chief executive of the Disability Trust Margaret Bowen is expected to give evidence.

Safeguards under the National Disability Insurance Scheme will be examined as part of the two-week hearing.

The hearing before Justice Jennifer Coate continues.

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