The parents of two babies left with brain damage have had charges against them thrown out because of a lack of evidence.

Just over three months after the twin babies were born prematurely in Wellington, hospital staff discovered both had injuries consistent with "severe shaking", a decision by Judge Peter Hobbs said.

In the Wellington District Court last week, Judge Hobbs dismissed the charges against Porirua parents Kyle Henare Hotai and Tunushia Wikitoria Schuster, who were jointly accused of two counts of failing to provide proper parental care.

The charges were dropped because there was no evidence to show Hotai and Schuster should have known the children needed medical care, as they did not have visible injuries.

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More than a year on from the injuries being discovered, nobody has been charged with causing them.

The twins were born on January 6 last year. Schuster initially cared for them while Hotai worked full time, but she began having trouble coping with them, and would disappear from the family home for periods of time.

"The twins were left in the care of friends and extended family. During this period of time, it is alleged that Ms Schuster was using methamphetamine," Judge Hobbs' written decision said.

In the early hours of April 15, 2017, Hotai awoke to feed and change the twins, returning to bed with a baby either side of him. Schuster was away for the night.

Hotai woke later that morning to find one of the babies lying on the floor gasping for breath. He picked her up and shook her, and she then went limp. While running to the neighbour's house to call 111, Hotai also slipped on the wet ground and dropped the baby.

He began CPR before an ambulance arrived.

Wellington Hospital staff discovered an old rib fracture and acute bleeding over the baby's brain, thought to be between a few hours and a few days old.

A blood test came back positive for severe bacterial infection.

There was also "chronic bleeding" across the surface of her brain believed to be weeks old, as well as more old rib fractures and retinal haemorrhages in both her eyes.

"The medical opinion was that [her] pattern of injury was best explained by her being subject to more than one severe shaking incident."

The other baby was also examined and was also found to have broken ribs and bilateral subdural haemorrhages - bleeding around the brain - of different ages.

The evidence was that both babies had suffered "non-accidental injury" on at least two occasions each.

There was no evidence as to who caused the injury.

The Crown has not charged Hotai for dropping the baby while trying to get help for her.

The twins were no longer in the care of their parents.

Oranga Tamariki - Ministry for Children Wellington/East Coast regional manager Grant Bennett said they were working with the family concerned and the children were safe in the care of Oranga Tamariki.

Detective Senior Sergeant Neil Holden of the Child Protection Unit called for anyone with information that might assist to contact police.

"The police Child Protection team endeavour to keep children safe, and consider success in a connected prosecution as an important, but secondary objective."

Police strive to get the best outcome for all parties, and this was aided by appropriate adult behaviour and "brave ownerships of issues by adults" so the wider situation can be addressed, he said.

"This may, or may not, involve prosecution."

Wellington Hospital clinical leader of child health Dr Andrew Marshall said it was "very likely" babies presenting with such injuries would suffer permanent brain damage of varying degrees.

"The long-term consequences can be severe."

It might not be clear for a few years how the children's brains have been affected, as some shaking victims display visible symptoms such as cerebral palsy, while others experience more subtle mental disabilities.

While sometimes young brains had a good repair capacity, "there will definitely be damage with that degree of injury," he said.

Spokeswoman for anti-domestic violence charity Shine, Holly Carrington, said there needed to be more education around the dangers of shaking babies.

"We need to get to the point as a society where there's enough education ... that no one can say that they didn't know.

"You can't shake a baby, there's so much potential for brain damage."

Schuster and Hotai have been contacted for comment.