Two Catholic charities have raised fears of bias as they launched a legal challenge against the choice of chairwoman for Scotland's public inquiry into historic cases of child abuse.

The Congregation of the Poor Sisters of Nazareth and the Daughters of Charity of St Vincent De Paul have lodged a petition for judicial review at Edinburgh's Court of Session objecting to the Scottish Government's appointment of Susan O'Brien QC.

Their action centres on Ms O'Brien's involvement in a case brought against the Poor Sisters of Nazareth at the House of Lords by two former residents of Nazareth House children's home in Glasgow who alleged they were abused in the 1960s and 70s.

Ms O'Brien acted as counsel for the former residents in their 2008 appeal which unsuccessfully challenged an earlier court ruling that the claims were time barred, or made too late.

Alastair Duncan QC, representing the charities, told the Court of Session: "The particular concern that my clients have is that Ms O'Brien had acted for individuals alleging abuse against them, that she had supported the allegations that were made by appearing as counsel for those individuals and that she is now being asked to adjudicate on the very same issues."

Mr Duncan said the allegations that arose in the House of Lords case were "almost certain" to be heard again at the public inquiry.

"On the same issue with the same parties, Ms O'Brien has moved from being an adviser to being a decision maker," he said.

"She was the adviser on how to take these allegations past the time bar problem to a successful outcome for her clients against my client.

"She is now to be the decision maker on that issue."

The House of Lords case did not involve the Daughters of Charity of St Vincent De Paul but that organisation has also been the subject of allegations of abuse, the court heard.

Mr Duncan told judge Lord Woolman that Ms O'Brien had acted in a number of other cases in connection with allegations of historic abuse.

He said the legal challenge was founded on an "apparent bias" rather than any assertion that she was actually biased against the charities.

The QC said: "That forms the basis of the objection - do the petitioners have a reasonable apprehension of bias on the part of Ms O'Brien?

"What is the public perception? Is there the possibility of unconscious bias as viewed by the objective bystander?"

Education Secretary Angela Constance announced Ms O'Brien's appointment last month and she is due to take up her post on July 1.

The inquiry will cover allegations of abuse of children in formal institutional care including faith-based organisations, children's homes and secure care as well as those in foster care, long-term hospital care and boarding schools.

It will have the power to compel witnesses to attend and give evidence, and the Education Secretary previously pledged that where crimes are uncovered the ''full force of the law'' would be used to bring those responsible to justice.

Survivors of abuse were consulted on who should lead the inquiry after two people appointed to chair a similar UK inquiry both stood down.

Home Secretary Theresa May had ordered the probe as part of her commitment to uncover the truth about long-standing claims of child sex abuse by powerful figures.

But Baroness Butler-Sloss stood down as chairwoman last July amid questions over the role played by her late brother, Lord Havers, who was attorney general in the 1980s.

Her replacement Fiona Woolf, the then Lord Mayor of London, resigned in October following a barrage of criticism over her ''establishment links''.

In February, Ms May announced that the inquiry would be chaired by New Zealand High Court judge Dame Lowell Goddard.