It is administered by an independent board, as opposed to a government authority, often based on some religion or ideology. Types of schools include Protestant, Reformed, Roman-Catholic, Islamic, and Jewish.
At the same time, it is within far-going control of the Ministry of Education and its Inspection. Special schools cannot charge tuition over the statutory rate, and they are subsidized on equal footing with public schools. They are notably distinct from private schools -- of which there are a small but increasing number -- which get no subsidies and can charge arbitrary tuition.
The special schools arose during the pillarization of Dutch society, when religious and secular parties fought over religious education and reached a rather elaborate compromise.