The inquiry is examining historical allegations of the abuse of children in care and has been taking statements from witnesses since last spring.
Officials said the first part of the second phase starting in autumn will focus on homes run by the Daughters of Charity of St Vincent de Paul, such as Smyllum Park in Lanark, Bellevue House in Rutherglen, St Joseph’s Hospital in Rosewell, St Vincent’s School for the Deaf/Blind in Glasgow and Roseangle Orphanage (St Vincent’s) in Dundee.
In early 2018, the inquiry will examine homes run by Sisters of Nazareth, investigating Nazareth House sites in Aberdeen, Cardonald, Kilmarnock and Lasswade.
A statement released on behalf of the inquiry said: “Evidence given at hearings will supplement written statements taken from witnesses in advance and documents which have been recovered by the inquiry team during the course of investigations.
“The inquiry will continue to take statements from survivors in private sessions and from a range of other witnesses, and urges anyone with information or experiences of establishments run by the Daughters of Charity of St Vincent de Paul or the Sisters of Nazareth to contact the witness support team as soon as possible.”
The first sessions of the inquiry will start on 31 May and will hear evidence from faith-based organisations, residential and foster care providers, expert witnesses, the Scottish Government and survivor groups.
They will take place at Rosebery House in Edinburgh and are expected to last about seven weeks.
They will hear evidence of the history and governance of large care providers of residential and foster care to children in Scotland and faith-based organisations, and whether there is any retrospective acknowledgement of abuse.
There will be evidence from Quarriers, Barnardo’s and Aberlour Child Care Trust.
The Church of Scotland/CrossReach, the Bishops’ Conference, the Good Shepherd Sisters and the Benedictines are among those who will give evidence.