A confrontation at the historic Sister Kate's site in Boorloo ended in a stalemate on Friday, with a group of Indigenous women remaining on the premises which is at the centre of a long-running dispute.

The site in Queen's Park was the location of Sister's Kates home, to which many Stolen Generations children were taken while it operated for much of the 20th century.

The land is owned by Beananging Kwuurt Institute (BKI), an agency of the Uniting Aboriginal and Islander Christian Congress (UAICC) which is affiliated to the Uniting Church.

BKI delivered services on the site, including essential household supplies, food, art classes, support for homeless people and domestic violence survivors, and other support services, to Indigenous community members but in December was effectively shut down by Congress, with the board having been suspended mid-year.

In recent years a successful BKI Art Group has emerged– led by WA Women's Hall of Fame inductee Lesley Murray – which had progressed to the point that some of the women and Elders were able to sell their own works, with many BKI artwork exhibited across Australia with the support of big corporates like Rio Tinto.

Earlier this month the UAICC and the new BKI board signed a Memorandum of Understanding with the WA Stolen Generations Aboriginal Corporation – Yokai: Healing Our Spirit – for new management of the site and the establishment of truth and healing centres. Yokai has a 12-month one dollar lease on the site.

On Friday morning, Yokai said in a statement that the organisation's board members and leadership, alongside "Sister Kate's Children's Home Survivors & Whadjuk Traditional Owners", would attend the site "to remove the unauthorised individuals". WA Police also attended when the current occupants refused to leave.

However, Police did not forcibly remove them.

Yokai chair Jim Morrison told National Indigenous Times that Yokai was "a third party" in the dispute, and the eviction did not go ahead due to the new BKI board not physically bringing relevant governance documents to the site.

"We are going through the correct procedures… we are doing things by the book, but were told yesterday we did not need to bring the paperwork," he said.

Dr Morrison said the situation was "frustrating" and that he understood a bailiff would become involved.

The women occupying the site, who include former Sister Kate's residents, were critical of the Uniting Church and Congress for following through on a notice posted on the site on Thursday warning of police intervention and possible trespass charges.

"They could have met with us, like we asked—not come down on us like a tonne of bricks," said Aunty Dorothy Ann Winmar Riley Hansen, a Noongar Elder and former cottage mother at Sister Kate's.

"Instead, they're forcing us out while we're in mourning, grieving at funerals."

Aunty Janet Garlett, a senior Noongar woman and spokesperson for the women, alleged the Uniting Church was using threats instead of peaceful dialogue, as was promised.

"We are the families of Stolen Generations children who were taken here. We deserve a say in this land's future," she said.

On Friday, as police and Yokai leaders arrived at the Sister Kate's site, the women revealed they had lodged a discrimination complaint with the WA Equal Opportunity Commission, and said this action compelled WA Police to seek legal advice as to the legality of removing and charging the occupiers with trespassing.

The group allege the previous BKI board's dismissal constituted sex, race, and political belief discrimination, which they said questioned the new actions of the new board—including its deal with Yokai, and BKI's legal authority over the land.

National Indigenous Times has previously reported on the alleged squandering of $5.5 million by the original BKI Board in 2007, which was supposed to fund social services for local Indigenous community members

"The Church is distracting from the truth – they still own this land under the new deal with Yokai," Aunty Janet said.

"We want healing, justice, and real self-determination… The Uniting Church must be held accountable and right past wrongs."

The Return Sister Kate's women requested the following of Yokai: No police intervention against Noongar women and supporters; Recognition of the discrimination complaint and a halt on all land deals until resolved; Urgent mediation with the Return Sister Kate's women's group to find a resolution; Return the land to self-determined Noongar ownership per Recommendation 41 of the Bringing Them Home Report.

Yokai now has a 12-month lease on the site, to engage with the community in relation to the future plans for the site, while the community services operating via the suspended BKI board have mostly ceased since the eviction notice on the former BKI in December.

Yokai said there was no obligation to include the women in the initial negotiations between the new BKI Board and Yokai.

Dr Morrison said earlier on Friday that he was disappointed the site had to be forcibly reclaimed.

"The people occupying the buildings and the land are not prepared to listen to Aboriginal cultural leaders with views different to their own," he said.

"Yokai has a legal entitlement to occupy the land and we are keen to get onto the site and commence consultation and planning to create a place of truth, justice and healing for all Stolen Generations survivors and their families."