The inquiry will look into problems at the new Royal Hospital for Children and Young People (RHCYP), which had been due to open this summer but is still not in use. A report last week blamed a tender error for the ventilation problems that delayed the opening.
The Queen Elizabeth University Hospital (QEUH), which opened in 2015, will also be included in the inquiry following concerns from affected parents over safety and wellbeing.
The inquiry will determine how vital issues relating to ventilation and other key building systems occurred, and what steps can be taken to prevent this being repeated in future projects.
Health secretary Jeane Freeman said: “The safety and well-being of all patients and their families is my top priority and should be the primary consideration in all NHS construction projects.
“I want to make sure this is the case for all future projects, which is why, following calls from affected parents, I am announcing a public inquiry to examine the new Royal Hospital for Children and Young People and the Queen Elizabeth University Hospital sites.
“The recent KPMG and NSS reports into the new Edinburgh Children’s Hospital will provide a significant amount of the underpinning evidence for the inquiry alongside the ongoing independent review into the delivery and maintenance of the QEUH.
“The current situation is not one anyone would choose – but it is one I am determined to resolve.”