More than 220 children who were removed from their families to keep them safe went on to be harmed in state care over a six-month period.
The new findings, the first from Oranga Tamariki's new reporting system on child harm, were described as "distressing" by chief executive Grainne Moss.
"It's really important that we keep children safe and on some occasions what this data shows is that we've failed to do that," she told the Herald.
In the worst cases, children had been raped or beaten. Several incidents led to criminal charges.
Oranga Tamariki, the Ministry for Children, set up the new reporting system last year, to replace the patchy, narrowly-focused one used by its predecessor Child, Youth and Family.
The new system is one of broadest and most detailed in any jurisdiction. It records abuse committed against a child by anyone, not just the caregiver, and in any location, not just within the child's placement. It records all incidents of harm, accidental and intentional, and ranging from over-zealous discipline of a child through to severe physical or sexual assaults.
As of June last year, there were 6350 children and young people in state care in New Zealand. Between July and September, 130 of them were found to have been harmed. Between October and December, 97 were found to be been harmed.
Some of the incidents were historical but were first reported during this period. A few children were harmed more than once. They were mostly likely to have been abused by caregivers, though many of the sexual assaults were committed by other young people or unrelated adults.
Children's Commissioner Andrew Becroft said the findings were "deeply disturbing" and "utterly unacceptable". But he said Oranga Tamariki had been bold in recording and revealing the full extent of abuse in state care for the first time.
"It's a courageous step to publish these and to not seek to hide as was often the case in the past. Now we know what we're up against, inarguably."
Becroft said the information raised questions about the level of support being given to caregivers, and underscored the importance of new minimum standards for care which were coming into force in July.
The new information allowed Oranga Tamariki to respond more quickly and effectively to protect children in care, Moss said. Immediate action was taken in every abuse case. In many cases the child was removed from the placement. Social workers and caregivers were sanctioned, and several criminal cases are ongoing.
One of the patterns which developed was that physical harm was usually driven by caregivers' difficulty in managing kids' behaviour, or by inappropriate use of discipline.
As a result, Oranga Tamariki was providing more training and support to caregivers.
Historic abuses of children in state care are soon to be investigated by a Royal Commission of Inquiry. The inquiry's scope is limited to abuse which occurred before 2000, though some advocates wanted a later cut-off.
Becroft said while the sector had improved significantly since 2000, the new findings "demolished" the "deluded" idea that abuse had suddenly disappeared.
"That is why we firmly submitted in our office that the Royal Commission should have discretion to investigate abuse right up until today's date - and indeed they have that discretion."
Moss said that in historical cases, many victims had complained that nobody listened to them or did anything about it.
"Whilst this report is distressing, the very strong message it sends is if you tell us we will take it seriously and deal with it immediately so we do not get something saying in 10 years' time … nobody did anything."