The Scottish Government ordered an immediate inspection of the Hamilton School in Aberdeen earlier this month after complaints from parents and staff about the nursery prompted a police investigation.
Following the inspection, the Government has ordered the school to be removed from the Register of Independent Schools which means that as of today it can no longer operate as a school.
The school said it is considering an appeal.
Last week, the Care Inspectorate served an improvement notice on The Hamilton School Nursery, requiring urgent changes around life-saving medication, nutrition and staffing.
The Care Inspectorate said it has "serious concerns" about the quality of care at the nursery, which is covered by separate legislation. It has applied to Aberdeen Sheriff Court seeking suspension of its registration and a hearing is scheduled for Wednesday.
During their visit to the school, HM Inspectors had to intervene in two lessons where they saw serious health and safety risks and referred three child protection cases to Police Scotland.
They concluded that the Hamilton School is failing in its duty of care to children and staff.
Earlier this month, two female members of staff, aged 25 and 65, were reported to the procurator fiscal after police investigations.
Minister for Learning Alasdair Allan said: "There is clear evidence from the HM Inspectors' report that there have been serious failings in the school.
"They have said it is simply not safe for children to go there and so we have had no alternative but to order the school closed immediately."
The Government said this is being taken forward "as a matter of urgency".
A Care Inspectorate spokesman said after the visit yesterday, the organisation remains "extremely concerned for the health, safety and welfare of children".
The Hamilton School caters for children from birth to 12 years old.
A Hamilton School spokesman said: "A lengthy letter from Education Scotland has been submitted to the school and we are considering this with our legal advisers.
"An appeal is under active consideration. We are stunned by this decision and don't believe it's in the best interests of the children, their parents or the 85 staff employed here.
"In nearly 40 years of business we have had thousands of satisfied parents and children and the majority of those whom we have spoken to over the past few weeks have remained happy with the school and have been very supportive."
Police Scotland said that their inquiries are continuing.