Two children with assault codes - one less than a year old - spent time in intensive-care units, although their reason for admission may have been unrelated to assault.
The figures were described as an only partial count for 2011/12 and did not include records of "short stays" in emergency departments.
Between 2006 and 2010, nearly 300 babies less than a year old were tagged with the codes at hospitals, while a 2010 report found New Zealand's rate of death from maltreatment of children was the fifth highest out of 26 OECD countries, with the largest proportion occurring in infants less than a year old.
Patrick Kelly, director of Starship hospital's child protection team, believed the ministry figures were "almost certainly a significant under-estimate" of true rates.
Dr Kelly was pleased Coroner Garry Evans had recommended specialised child protection teams in all health board districts.
"It's hard to predict what will bring the rates down - but uniformity and consistency will help," Dr Kelly said.
Mr Evans has also called on authorities to consider introducing laws that would see health professionals being legally obliged to report instances of physical abuse to CYF, and require health and education authorities to have a statutory responsibility for the protection of children and to work alongside child protection agencies.
Social Development Minister Paula Bennett said although none of the recommendations came as a surprise after having been raised previously, she would examine them in detail.
Children's Commissioner Russell Wills said systems in place to deal with abuse were close to international best practice.
Dr Wills believed the change needed was a societal one.
"What we want is primary prevention - and that is going to require all adult New Zealanders standing up when they see violence happening."
Meanwhile a study shows that Maori children are nearly 30 per cent more likely to be admitted to hospital and twice as likely to die from "avoidable conditions".
The research was led by Northland public health physician Clair Mills with Auckland University economist Rhema Vaithianathan and Faculty of Medical and Health Sciences academic Papaarangi Reid. It found that avoidable deaths of Maori children were costing at least 67 lives and about $200 million per year in economic impact.
