What is the difference between public kindergartens and private kindergartens / nurseries?

Public kindergartens are usually run by local municipal govt authorities. Private kindergartens are run by private entities and they might be “endorsed” by the local municipal govt. or they might not. 58% of kindergartens are private and account for 77% of all enrolled children.   Other children attend govt supervised day-care centres called hoikuen. Preschools private or public take care of infants and toddlers. Together, over 90% of all preschool age children in Japan are enrolled in these two types of preschools and kindergartens.

Compulsory education in Japan only covers primary (elementary) and lower secondary (middle school) which is why most kindergartens (and preschools) are private.
[The obligation for compulsory education is stated thus:
“Among the 6.3.3.4 years of education, every child must enter and graduate from an elementary school and a junior high school, as this is compulsory education. Compulsory education is an obligation for Japanese citizens. However, children of age six to 15 with foreign citizenship may enter or transfer to local elementary schools or junior high schools with same expenses as Japanese citizens, regardless of their nationality.”–  Source: The Council of Local Authorities for International Relations
NOTE compulsory education only covers Japanese citizens: The Tokushima municipal govt’s Living Guide says “There is no compulsory education for non-Japanese children resident in Japan, but if you wish your child to go to a Japanese elementary or junior high school, you should consult with your local Board of Education.”]
Even if kindergartens are privately run, the connections with the central govt MEXT are strong.
1) MEXT(Ministry of Education, Culture, Sports, Science and Technology)’s 1990 Course of Study for preschools has applied to local preschools and kindergartens, though from January 2010 all preschools and kindergartens start following the International Preschool Curriculum which I guess means incorporating more academic goals.
2) Kindergartens are predominantly staffed by young female junior college graduates – institutions that are supervised by MEXT, though strangely these teacher training colleges are not part of the official education system.

Note: Oversight for nurseries is different – not by MEXT but by the Ministry of Health, Labour and Welfare.
The Tokushima Living Guide has the following additional information on types of kindergartens and nurseries:
(1)Nursery School
Types:
Public nursery schools, run by the local municipal authority
Privately run nursery schools (this includes those endorsed by the local municipal authority, and those that have not received official endorsement)
Age range: This can vary depending on the school, but is usually from around 2 months of age, until 5 years old (elementary school age).
Public Nursery Schools / Private Nursery Schools Endorsed by the Local Municipal Authority
Eligibility: children are eligible for a place at a nursery school if they cannot be cared for at home, for reasons such as parents’ work or family circumstances.
Fees: depends on the family’s income
Admission at the start of the school year (April): apply at your local municipal office, or at the nursery school, in December or January.
Admission during the school year: if there are spare places, it may be possible for a child to start nursery school at any point during the school year, so please ask at your local municipal office.
It may not be possible for all applicants to get a place at the school of their choice.
Private Nursery Schools Not Endorsed by the Local Municipal Authority
Eligibility: no special requirements
Fees: a set cost, regardless of income
Application: you can apply directly to the school of your choice.
(2)Kindergarten
Public Kindergartens
Eligibility: the child and parent / guardian must live in that city, town, or village.
Admission: please apply directly to the kindergarten in around December.
Private Kindergartens
There is an interview and test for those wishing to apply.”

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