An independent review examining water contamination and other problems at Glasgow's largest hospital will be published in the spring.
Health Secretary Jeane Freeman faced questions from MSPs after details emerged of the deaths of two children.
Both were treated in a ward at a Glasgow hospital which was later closed because of water supply problems.
The health board has apologised for the distress caused to parents who have complained of a lack of information.
The deaths have also put Ms Freeman under pressure but on the campaign trail First Minister Nicola Sturgeon said the health secretary has her support.
Ms Freeman is due to make a statement to the Scottish Parliament about the Glasgow hospital on Wednesday.
Ms Freeman told MSPs on Holyrood's health committee the ongoing review into the Queen Elizabeth University Hospital campus, which includes the Royal Hospital for Children, had taken evidence on water contamination.
The health secretary said she expects a separate public inquiry, which will examine safety and wellbeing issues at the QEUH and the new children's hospital in Edinburgh, will also look at water contamination.
That inquiry will determine how vital issues relating to ventilation and other key building systems occurred and it will also look at how to avoid mistakes in future projects.
MSPs were told a chairperson will be announced before the festive recess.
The committee also heard an Independent National Whistleblowing Officer for Scotland will be appointed so NHS staff can speak up when they need to and have no qualms about doing so.
Last week it emerged Milly Main, 10, died on 31 August 2017 while recovering from leukaemia treatment.
The child's death was made public after Labour MSP Anas Sarwar was contacted by a whistleblower.
Milly's mother later told BBC Scotland that she was "100%" convinced her death was linked to water contamination issues.
NHS Greater Glasgow and Clyde (NHSGGC) has insisted it was impossible to determine the source of Milly's infection because there was no requirement to test the water supply at the time.
Pressure on the board intensified on Sunday when it was revealed police are investigating the death of a three-year-old boy three weeks before Milly.
Both children were patients at the Royal Hospital for Children.
NHSGGC said they had fully investigated and shared their findings with the boy's family but the child's mother later described the board's media statement as "highly inaccurate".
On Monday Ms Freeman told BBC Scotland putting the health board into special measures was an option and she would make a statement to the Scottish Parliament on Wednesday.
The powers were last used on NHS Tayside in 2018 and mean the Scottish government takes a more direct role in management.
In a letter to the health secretary on Tuesday Mr Sarwar condemned the board's handling of the cases as "utterly disgraceful" and called for whistleblowers' jobs to be protected.
'Not fully transparent'
The MSP wrote: "It is clear that they [the health board] are not fit for purpose. They have lost the trust of the families and NHS staff connected to these revelations.
"I also don't believe that they have been fully transparent with you. They cannot be left to investigate themselves. I implore you to please take control of this situation and put them into special measures."
In response to reports about the boy's death and the police investigation, a NHSGCC spokesman said: "We have already provided information to this family but are sorry that they have further questions.
"We fully investigated this child's death at the time and also asked for two independent experts to investigate the case, the outcome of which has been communicated to the family.
"We are absolutely committed to providing patients and families with information and ensuring they get answers to the questions they have. In this case the full findings were shared with the family."
But on Sunday Labour's health spokeswoman Monica Lennon said she had been in contact with the child's mother.
Ms Lennon said: "She disputes the accuracy of their investigations and reports and is in receipt of documentation that confirms bacteria was present in the showerhead within her son's hospital bathroom."
The MSP said that when the mother last met officials from NHSGGC she walked out of the meeting and advised them she would be taking legal action.
Last week a whistleblower revealed that a doctor-led review had identified 26 infections at RHC during 2017 which were potentially linked to contaminated water.
The £842m Queen Elizabeth University Hospital "super hospital" has faced a number of problems since it opened in 2015.
Two cancer wards at the adjoining children's hospital were closed last year amid concern about infections and investigation of water supply issues, with patients decanted to the adult hospital.
In January it emerged that two patients at the QEUH had died after contracting a fungal infection linked to pigeon droppings.