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 ordered on Friday that the school be removed from the Register of Independent Schools.
The Care Inspectorate served an improvement notice on the school's nursery, which is covered by separate legislation, and applied to Aberdeen Sheriff Court seeking suspension of the nursery's registration.
At the weekend, a nursery spokesman said parents had been told it would not reopen. The Care Inspectorate said it had decided to make its nursery inspection concerns public due to "intense" public interest.
The interim report said medical information on children was not kept up to date with parental consent forms expired in some cases, and some children as young as 12-months-old were left to feed themselves at lunchtimes when they were unable to do so.
Notes on allergies at meal times were also mixed up. The report said: "We also saw a menu plan designed for one child with allergies that contained details of another child's dietary requirements."
Dangerous cleaning products such as air fresheners, plastic bags and medicated creams were also stored within reach of children in the nursery toilets.
Annette Bruton, chief executive of the Care Inspectorate, said:"The decision of the provider to close the nursery is, we believe in the best interests of children, although we know this makes it a very difficult time for parents and families."