Waikato DHB child protection team nurse co-ordinator Gaye Andrews said the abuse figures could be skewed if staff hadn't notified the child protection team.
She said head injuries to babies from being shaken - usually in the first year of a child's life - were a common phenomenon.
Ms Andrews also worked in the hospital's clinic, which saw about 60 children a year who had been badly neglected, severely physically abused or were there for sexual abuse examinations.
"My take on it is thank God someone has found them [early] enough to send them or worry about them ... We know that every five weeks one child in New Zealand is murdered by someone that loves them - that's a pretty grim statistic."
All cases of suspected/definite child abuse identified by Waikato DHB staff are referred to Child Youth and Family and/or the police.
Child Matters chief executive Anthea Simcock said head injuries were quite common, particularly in the younger, more vulnerable age group, and also among older children.
"One is one too many for a child, so absolutely we need to be doing a lot more to reduce that," Mrs Simcock said.
"We need to be getting involved really early to identify which children are at risk."
Although the rising figures were alarming, Mrs Simcock said they could result from increased focus on diagnosing assaults during the same three-year period.
This meant that staff were "seeing what was not seen before and that those children as a result will be protected rather than being sent home to be possibly re-abused."