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.
The facility, which has the same building contractor as the Glasgow super-hospital, 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."
Ms Freeman will speak in the Scottish Parliament on Wednesday to confirm "a full statutory public inquiry with all the power that brings".
She told BBC Scotland's The Nine: "I will make it clear in the chamber tomorrow that there will be a public inquiry and broadly what its scope is.
"I'll come back to our Scottish Parliament with the full remit, with the name of who will lead that and with the timeline. That's normal."
She added: "What the public inquiry will be looking at is how in the NHS we design, contract, build and maintain our major infrastructure.
"And how we take into that all the available evidence - in terms of infection prevention and control - and how we make sure that our buildings are compliant with national standards and guidance.
"It will also, I am sure, make recommendations to us - particularly about what more we need to do in order to insure that all of that is met to the best quality that we can."
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.
The Scottish Conservatives said the public inquiry was "long overdue" and insisted it had only come about because "the SNP hierarchy has become fed-up of negative headlines".
The party's health spokesman Miles Briggs said: "The ongoing problems at both hospitals are consequences of SNP negligence of the NHS which has gone on for more than a decade.
"It is now vital that the public inquiry reports as soon as possible and considers the decisions taken around these projects by all four SNP health secretaries."
Scottish Labour's Monica Lennon said the inquiry was "the only way to get to the bottom of this outrageous series of errors".
'Not fit for purpose'
She added: "Children in Scotland are being let down because the hospitals they were promised are not fit for purpose.
"We have two hospitals built by the same contractor that are mired in controversy, and all the while patients are suffering.
"The public need to know the truth of what has gone so badly wrong at these two vital hospitals."
The Scottish Lib Dems said public trust in the projects needed to be "urgently restored."
Spokesman Alex Cole-Hamilton MSP said: "Quite simply, we cannot have young patients being treated in facilities that are not up to scratch.
"It is vital that this public inquiry now moves forward in a way that complements and does not further delay the opening of the Sick Kids hospital."
Alison Johnstone, for the Scottish Greens, welcomed the announcement but said the health secretary must not use the inquiry as "an excuse to avoid legitimate parliamentary scrutiny".
She added: "The Scottish government must ensure that the health and wellbeing of patients and staff is paramount going forward, and provide adequate support to all those who have been affected at both sites.
"There are also significant questions around the private finance schemes used to fund these projects and I hope that is an area the inquiry can examine."