Health Secretary Jeane Freeman said she overruled NHS Lothian's plans to open the new children's hospital in Edinburgh next week.
The £150m building in Little France was due to open on Tuesday but is now subject to indefinite delays.
The decision not to open the landmark hospital came after last-minute inspections found safety concerns over its ventilation system.
It is understood the health board had been considering a partial opening.
Ms Freeman has ordered an investigation into the problems with the new building and said patient safety had to come first.
She told BBC radio's Good Morning Scotland: "NHS Lothian were looking at options, they had not made a decision about what they wanted to do.
"I took the decision that it was not safe to open the hospital next week in any respect until I'd been assured for patient safety that every other area of that hospital met national standards."
Asked if she had overruled the health board, Ms Freeman said: "Yes, I have."
The health secretary said she was informed on Tuesday that the "final validation check" of the ventilation system in Critical Care at the new Royal Hospital for Children and Young People was not meeting national standards.
She said: "Because this was picked up so late I want to be sure that all other safety checks in the rest of the hospital are also conducted again.
"The decision I took was that it was too great a risk."
The new 233-bed hospital will form part of the Royal Infirmary of Edinburgh campus, providing care for children and young people to about 16 years of age.
It will also have 10 theatres and a children's emergency department.
The site, which also includes Clinical Neurosciences and Child and Adolescent Mental Health Services, had been due to open in 2017 but a series of problems pushed that back.
The building shares the same main contractor and design as the Queen Elizabeth University Hospital in Glasgow, which has also had problems with ventilation systems.
Ms Freeman was asked in parliament last month if NHS Lothian had been assured the same problems did not exist at the new site.
The health secretary said NHS Lothian told her it would not take ownership of the building until it was "absolutely assured" those steps had been taken.
She said she now needed to find out why the health board was so confident the hospital was meeting standards "when self-evidently in Critical Care it certainly wasn't".
Ms Freeman said she had asked for an audit of the safety checking process so she could identify where the mistake had been made.
The main contractor building the hospital, Multiplex, issued a statement saying its work was signed off as complete by the Independent Certifier on 22 February, when it handed over the building to NHS Lothian.
The health secretary said: "There's no indication at this point that any fault lies with the contractors themselves."
Ms Freeman said she did not know how long it would be before the new hospital was opened but the old Sick Kids hospital would remain in use.
She said there was a helpline available for people who had appointments planned at the new hospital.
Ms Freeman said she should have the results of the additional safety checks "very soon".
If everything was ok with the rest of the site, there could be a "phased move" of other units such as outpatient services and neurosciences.
She said work was under way to identify what upgrade was needed to the ventilation system in Critical Care.
It was "likely to take months rather than weeks" before Critical Care and the Emergency department could open, she said.
Ms Freeman admitted that there could be difficulties with any move if it was delayed until the winter months.
"At this point I can't say when Critical Care and the Emergency department will move into the new site," she said.
Unison Scotland, which represents many NHS staff, said union members were feeling "exasperated, shocked and concerned".
A dedicated helpline has been set up on 0800 028 2816. This will be operational from 12pm on Friday and will run until 10pm. After that the line will be operational from 8am until 10pm during the week and from 9am to 5pm on Saturdays and Sundays.