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 at the faith-based centre, and has referred the matter to a parliamentary inquiry.
In a statement, the Esther Foundation confirmed it had entered administration and blamed a "media campaign" which it said had caused significant reputational damage.
"Our funding base has reduced to the extent that we are likely to become insolvent in the very near future and accordingly under law, we cannot continue to operate," it said on Wednesday.
"The predicted outcome of this administration process will be the closure and winding up of the foundation."
The foundation said it would seek an appropriate professional organisation to ensure continuity of care and alternative support for the women and children in its care.
Administrator Mervyn Kitay of Worrells said donations had been withdrawn from the foundation in light of the negative publicity.
He said the limited remaining funds appeared sufficient to keep the centre open for several weeks.
"As a consequence, no current resident will be required to vacate in the near term, unless of course they elect to do so voluntarily," he said.
Anyone with a criminal complaint is encouraged to contact police.
Women's Interests Minister Simone McGurk has referred the matter to parliament's education and health standing committee.
She told parliament her office had received dozens of serious complaints, spanning from 2004 to 2020.
They included Aboriginal residents being denied the right to practice their culture, likened to "being possessed by the devil".
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.
In a statement earlier this month, the board of the Esther Foundation described the allegations as confronting and distressing.
"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.
The foundation does not receive operational funding from the state government but was provided with two properties under a peppercorn lease.
That arrangement is being 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 this month.
Prime Minister Scott Morrison announced a $4 million grant for the facility, linked to several Pentecostal churches, during a visit to Perth in 2019.
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