The Education Ministry has found evidence of problems including abuse of children, poor health and safety and inappropriate staff behaviour in early childhood centres.
The ministry's latest complaints summary showed it upheld 163 complaints in 2016, including 12 about physical or emotional injuries to children, 12 of inappropriate staff behaviour and eight of centres operating with too few staff.
It says 23 of the complaints resulted in centres losing their licence in 2016, and 24 complaints resulted in the ministry placing centres on suspended or provisional licences.
The ministry involved police in 27 cases, Oranga Tamariki the Ministry for Children in 22 cases, and the Education Council (which investigates complaints against teachers) in 14 cases. It referred two cases to the Serious Fraud Office.
In total the ministry received 331 complaints in 2016, 11 fewer than in 2015.
"We investigated 245 of the 2016 complaints. A further 86 did not require investigation. These were either resolved at the source, referred to the service's own complaints process, referred to another agency or withdrawn," the ministry's report said.
"Of the complaints investigated by the ministry, a total of 163 were upheld, meaning that standards had not been met or the investigation found something that the service was required to improve. In 2016 we investigated and upheld more complaints than in previous years."
The report showed that many of the upheld complaints involved health and safety (46), or management and administration problems (34), but others included the standard of education (22), teachers' behaviour (12) and unsafe premises (18).
The ministry said 24 of the complaints resulted in staff leaving the early childhood service.
The figures were published a month after an investigation by RNZ's Insight programme reported allegations that some early childhood centres were providing sub-standard care and education, including operating with fewer teachers than required.
The ministry said it also received 152 notifications of incidents such as accidents at early childhood centres in 2016.
"In May 2016, we made it a requirement for services to let us know when a serious incident, injury or illness involving a child has happened that must be reported to another agency," it said.
The incidents resulted in the ministry cancelling the licence of one centre, suspending the licence of another, and placing nine centres on provisional licences.