The case was later dropped due to fears that the accused's disability was too serious to enable him to comprehend the charges against him.
An investigation by the Victorian Ombudsman, released in September, found that despite ongoing threats to Matthew, the alleged perpetrator continued to live at the Autism Plus facility.
Ombudsman Deborah Glass said "repeated failures" by Autism Plus and the Department of Human Services, "both by individuals and systemically, contributed to an unacceptable risk of significant harm to other clients, staff".
Matthew's mother, Maria Thomas, said she wanted justice for her son and all those who may have been harmed at the emergency facility. She said she would keep pushing until the facility was shut down.
"My son was raped there," Ms Thomas said. "How many disabled people have been raped there?
"They are just making a profit from disabled people. They failed my son. The Department of Human Services failed my son."
The Ombudsman found that Autism Plus, a for-profit provider, reduced the alleged perpetrator's night supervision from two staff to one for "financial" reasons, despite the organisation identifying the accused needed "two-person restraint" to stop any assaults. But Autism Plus told Fairfax Media it was only funded for one staff member in a "sleep-over capacity".
The report also stated that Autism Plus failed to notify some families of abuse until forced to by the Ombudsman.
Ms Glass said the investigation raised serious questions about the suitability of a service provider that received significant public funds. In 2014-15, Autism Plus received more than $5 million from the department to deliver its services.
Ms Glass also blamed the department, saying: "It is clear that DHHS did not respond to the concerns raised by [Matthew's] family by providing any alternative placement options for either young person".
Kevin Stone, who heads Victorian Advocacy League for Individuals with Disability, said they supported the parents' calls for the minister to act urgently.
Mr Stone said the board of Autism Plus should be stood down immediately and replaced with an administrator.
"What has been made abundantly clear is that these vulnerable people have been failed on every front," he said.
Minister for Disability Martin Foley said the report showed the families affected had been treated very badly and this was unacceptable.
"In response to these allegations, I will consider all options available to ensure the safety and wellbeing of clients – because the rights and safety of people in the care of others is my priority," Mr Foley said.
The government has moved to discipline Autism Plus after a review found several problems including with the firm's governance and staff training. No new clients have been placed at the agency since April.
Autism Plus general manager, people and information, Mathew Willis, said they had met with the department, were "advocating strongly", and effectively doing everything within their power to get the accused moved and had even encouraged the Thomases to contact VALID to see if they would also advocate on their behalf.
The Ombudsman's report also states that the accused admitted to sexually abusing a man known as Steven. His mother, Anne Mallia, said lives were being put at risk while the facility remained open.
"I cannot understand what else does the government needs before they shut this organisation down," Ms Mallia said.
"I don't sleep ... knowing ... that there are other human beings under their care."