Yesterday Jeane Freeman told the Scottish Parliament that the hospital, which was originally due to open in 2013, would now be delayed by another year while a ventilation system in the critical care unit was repaired. The work required will cost an extra £16 million, while the running of the old hospital as well as the new Sick Kid's will cost another £7m.
Today amid demands for a public inquiry after conflicting previous assurances that the hospital was on track to open in July, the First Minister was forced to defend Ms Freeman, who she said had taken "appropriate action".
At First Minister's Questions she said she "shared" the anger at the new delay, but that her government and Ms Freeman were doing the "responsible" thing by "rectifying the issue".
Scottish Tory interim leader, Jackson Carlaw said it was time for "heads to roll" after "four health secretaries, blunders, and cost over-runs - yet it was just yesterday the Scottish Government decided to appoint a troubleshooter to sort this mess out - isn't it too little too late?"
He added: "The ongoing problems over the last decade in relation to the Sick Kids project have been well publicised. Yet it seems SNP government ministers chose either not to know, or simply failed to ask, about the full extent of these issues until way too late.
“This has been an absolute shambles. The Sick Kids hospital was supposed to open at the end of 2012. Since then, more than 300,000 children in A&E alone have been denied access to the new hospital they and their parents were promised.
“This saga is sadly all too common. Ministerial assurances are given, completion dates pushed back then costs spiral out of control.
“Yet, at the end of it all, no-one is held to account. I think, the country thinks, for once heads should roll don't you?
Nicola Sturgeon admitted that the situation was "unacceptable" but avoided answering whether anyone would ultimately be held accountable, saying due process had to be followed.
She added: "The Health Secretary set out yesterday the work that will be done to establish issues of accountability and it's important that is done in line with due process.
"The focus is on making sure the rectification work is done. To say that I and the Health Secretary are angry about this situation would be an under-statement. The focus of the Scottish Government is on putting this right. The Health Secretary made very clear yesterday, that we would not allow the hospital to open until we're satisfied with patient safety."
She added: "We have escalated our oversight to Level 4, which means there will be closer scrutiny and oversight.
"But the issue that has resulted in the delay relates to the critical care ventilation system which only came to light at the start of July this year if Jackson Carlaw is telling me he knew about that before then why didn't he bring it to anyone else's attention because I didn't know about it and the Health Secretary didn't know about that. That is the issue that has prevented the hospital opening now. That is the issue the Health Secretary is focused on rectifying."
Ms Sturgeon also reiterated that the Scottish Government will establish a new national body, a centre of excellence to oversee the construction of large public infrastructure. She added: "I deeply regret the hospital will be opening extremely late.
"Lessons absolutely have to be learned from this. I absolutely agree this is an unacceptable situation, but our focus is patient safety and making sure these issues are rectified which is what the public would want to see."
Scottish Labour leader Richard Leonard also raised the growing problems at the Sick Kids and the Queen Elizabeth University Hospital in Glasgow, and demanded a public inquiry into the "abject failure of governance and government".
He said: “We have a children’s hospital in Edinburgh that can’t open its doors. We were reminded at the weekend that we have a hospital in Glasgow, built by the same contractor that has been closing its doors to a children’s cancer ward.
“Audit Scotland published a report saying there needs to be a review of ‘whole-project contracting’.
“We need to get to the bottom of this. We need full public transparency to restore public trust. So what will it take for the First Minister to finally listen and deliver a full public inquiry?"
Ms Sturgeon said that while Mr Leonard was right to "point out the issues with the Queen Elizabeth and the problems now with the Sick Kids hospital",
She stressed that the Scottish Government had previously had a "firm expectation" that the hospital would open in July as "all the previous issues had been resolved. An issue then came to light that hadn't previously been known to us."
"The Scottish Government will continue to do the work and take the action to rectify the issues that have been identified at the Sick Kids hospital that is the responsible thing to do. I share the anger the patients and staff have about this thoroughly unacceptable situation.
"The health board's responsibility was to ensure that this hospital was built to the right specifications and in this case it hasn't discharged that responsibility and there are questions that still require to be asked in that respect."