A public inquiry will be held to examine safety and wellbeing issues at the new children’s hospital in Edinburgh and the Queen Elizabeth University Hospital in Glasgow.
The inquiry will determine how vital issues relating to ventilation and other key building systems occurred.
It will also look at how to avoid mistakes in future projects.
Edinburgh’s Royal Hospital for Children and Young People had been due to open in 2017.
It will now not be ready until next autumn at the earliest.
Health Secretary Jeane Freeman said: “The safety and wellbeing 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.”
She added: “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.”
In January, it was confirmed two patients had died after contracting a fungal infection caused by pigeon droppings at the Queen Elizabeth University Hospital.
The health secretary later ordered a review of the design of the building and said there was an “absolute focus on patient safety”.
Meanwhile, the new £150m Royal Hospital for Children and Young People in Edinburgh has been dogged by delays over health concerns.
The hospital was supposed to open in 2017 – but will now not be ready until next autumn at the earliest – after problems with the specification of the ventilation system.
First Minister Nicola Sturgeon previously said she “deeply regrets” the hold-up, with opposition parties calling for “heads to roll”.
The opening date was put back when last-minute inspections found serious problems with the ventilation system in the facility’s critical care unit.
A report published earlier this month said £16m of repairs were needed to fix the ventilation and other issues that had been identified, with the work expected to take at least a year.
Inquiry into safety and wellbeing concerns at two hospitals