The Congregation of the Poor Sisters of Nazareth and the Daughters of Charity of St Vincent de Paul are seeking for Ms Susan O'Brien QC to be replaced as chief of the public inquiry into historical abuse.
It's because Ms O'Brien previously represented two people who claim they were abused at the Nazareth House care home in Glasgow in the 1960s and 70s. Nazareth House was owned and ran by the Poor Sisters.
In 2008, courts ruled that their claims were made too late.
Alastair Duncan QC, who is representing the charities in the Scottish Court of Session, said: "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."
According to The Telegraph newspaper, the Poor Sisters has had more than 300 legal claims of abuse made against it.
A spokesman for the Scottish government told Premier: "Ms O'Brien's appointment has been received positively by many people, including survivors.
"She is an experienced Advocate whose considerable knowledge and expertise was an important consideration in making this appointment.
"We are confident that her appointment is sound in terms of the Inquiries Act and that she will lead a fair, thorough and honest Inquiry."
