Former residents of the Esther Foundation have claimed they were denied food, medication and health services, prevented from seeing their loved ones and asked to give guardianship of their children to the facility's staff.
The WA government says it is also aware of allegations of sexual assault and other criminal offences.
Women's Interests Minister Simone McGurk has referred the matter to parliament's education and health standing committee.
The committee will not investigate alleged criminal actions but will focus on the regulation of the facility and other similar institutions, and the organisation's response to the concerns.
Anyone with a criminal complaint has been encouraged to speak to police.
"My ministerial office has received dozens of complaints, and the allegations are of a consistent and serious nature," Ms McGurk told parliament on Thursday.
The complaints, which she said spanned from 2004 to 2020, included Aboriginal residents being denied the right to practice their culture which was likened to "being possessed by the devil".
It was also alleged there was an absence of qualified staff.
In a statement earlier this month, the board of the Esther Foundation described the allegations as confronting and distressing.
It said the organisation had been overhauled more than two years prior and had parted ways with its founder and managing director.
"We sincerely and without reservation apologise to these women and any others who have been hurt or have experienced abuse in any form," the statement said.
"We are taking decisive steps to learn more about what happened in the years under the former leadership, bring resolution to anyone affected where this is possible and to ensure the safety and wellbeing of all our current and future participants."
Ms McGurk said the foundation did not receive operational funding from the state government.
It was provided with two properties under a peppercorn lease which will be reviewed.
"I also understand that state government agencies may have made referrals to this facility in the past, however we have emphasised to the relevant agencies that this is not appropriate going forward," Ms McGurk said.
Prime Minister Scott Morrison announced a $4 million grant for the facility, linked to several Pentecostal churches, during a visit to Perth in 2019.
The committee will report by December 1.
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