A study, led by Associate Professor Michael Baker and Cathryn O'Sullivan, found there were 547 cases of serious skin infections, such as cellulitis, abscesses and impetigo, per 100,000 children last year compared to 298 per 100,000 in 1990.
On average more than 100 children a week are admitted to hospital for treatment of skin infections, with most needing intravenous antibiotics and one-third requiring surgery.
Prof Baker said the study presented a "distressing picture for our children".
"We already had high rates of these infections compared to other similar countries," Prof Baker said.
He said the skin infections caused children unnecessary suffering and were "highly preventable" with early treatment by GPs.
The high rate of serious skin infections also cost district healthbBoards about $15 million a year and reduced hospitals' capacity to treat other surgical conditions.
The study found that nearly three times as many Maori children and four times as many Pacific Island children developed serious skin infections compared to other ethnicities.
Cases which required hospital treatment were just the "tip of the iceberg" with an estimated 60,000 children visiting GPs every year for treatment of skin infections.
Although the research did not look into causes behind the rise in infections, Prof Baker said it could be linked to rising income inequalities.
"More research is essential so we can identify the causes of this health problem, introduce preventative measures and improve early treatment," he said.