The Care Inspectorate and Education Scotland are looking into complaints about the Waldorf School Kindergarten in Aberdeen.
Issues around staffing are also being investigated.
The latest investigation comes after another private institution in Aberdeen, the Hamilton School, was closed by inspectors due to concerns over care.
A Care Inspectorate spokesman said: "We have received complaints around staffing and the care of children at the Aberdeen Waldorf School Kindergarten.
"We are currently investigating these issues and the outcome of our investigation will be published in due course.
"Because concerns have been raised about the school as well as the nursery, we are also carrying out a focused joint inspection with colleagues from Education Scotland over the next few days.
"Our first priority must always be the safety and well-being of children. Anyone with concerns can contact our helpline on 0845 600 9527."
The Waldorf School was founded in 1977 and was originally based in Aberdeen city centre but moved to an eight-acre campus in the Cults area in 1997.
An Education Scotland spokesman said: "Education Scotland has today commenced an inspection together with the Care Inspectorate of Aberdeen Waldorf School.
"Once the inspection is complete a Parental Letter detailing the findings will be published on our website."
The Hamilton School in Aberdeen was shut last month after inspectors said they were not confident pupils were ''safe and well cared for''.
The Scottish Government intervened after complaints from parents and staff prompted a police investigation.
The Hamilton School had 105 pupils and the nursery cared for 225 children. A disused primary school was re-opened to accommodate some of the pupils.