A judge has awarded $60,000 to the parents of a baby girl wrongly seized by welfare authorities.

The young couple, from Dunedin, have told the Sunday Star-Times of their harrowing two-year battle to regain custody of the girl, who was taken by Child, Youth and Family at just 14 weeks because the agency wrongly suspected she'd been abused.

In fact, the baby's multiple fractures were the result of rickets, caused by a lack of Vitamin D.

The pair were forced to go to court to prove they hadn't abused the baby.

The couple, who cannot be named because of Family Court suppressions, took their daughter to a doctor in 2011 after she began "vomiting and twitching".

The doctor suspected a bowel obstruction and arranged for the baby to be admitted to hospital. An MRI in hospital revealed the baby had a fractured skull, ribs and limbs.

The parents were interviewed by police and two days later, without notification, Child, Youth and Family applied for interim custody, which was granted.

Three days later tests showed the baby had severe vitamin D deficiency and rickets - a Victorian era condition, which can lead to fractures and deformity of bones. The couple thought at that point their daughter would be returned to them.

But when the case went to the Family Court, doctors were at odds over whether the infant's injuries were caused by trauma or rickets. A Family Court judge ruled in favour of the CYF decision to remove the baby.

Judge John Coyle said there was no evidence the "doting parents" were mistreating their daughter, but rejected rickets as a cause and said he could only conclude one of the parents caused her broken bones.

The baby was sent to live with her paternal aunt. Her parents had to sell their house in Dunedin and move to the North Island so they could continue to see her on supervised visits. The couple was able to force an appeal of the original decision with new evidence from a case in Britain.

In April 2012, two British parents were cleared of killing their 4-month-old son, Jayden Wray, who inherited rickets from an undiagnosed vitamin D deficiency in his mother and died from a head injury in 2009. A London Court ruled the boy's injuries were caused by rickets and granted the parents custody of their daughter, who had been in care since birth.

Last year Justice Graham Panckhurst, after seeing the new evidence, ruled in favour of the couple and returned their daughter to their care.

In his ruling he said in the light of new evidence he was satisfied there was "heightened uncertainty" about the cause of the child's injuries. He said the treatment of the parents and removal of the baby "provide cause for concern".

"It is very unlikely that these parents . . . deliberately inflicted the injuries."

Last week the family was awarded legal costs of more than $60,000.

By email, the couple said their world would "never quite feel safe again, although finally having our daughter back with us is starting to heal the wounds.

"Child abuse is a terrible thing, but being accused of harming your child when you are innocent is also terrible. And it could happen to any parent, at any time. It took determination and belief in each other as people and as parents, as well as amazing, enduring support from our family and friends and the incredible hard work of our lawyers for us to win this battle."

The couple said they had some understanding of the medical system and spent hours researching rickets and finding medical experts to speak on their behalf.

"It is hard to imagine how such a battle could be won, if the accused parents were without this knowledge, or were without a family who were willing and able to put themselves in debt to assist with legal costs."

They hoped their case would "encourage the medical community to be able to consider other diagnoses, and to admit that they do not always have all the answers".

Family law expert Mark Henaghan, of the University of Otago, said the trauma suffered by the family was "terrible" but the authorities acted correctly.

"I don't think anyone overreacted here or acted in a zealous way. It was a rare condition and a rare situation so I think everyone was a bit mystified by it.

"You have got a child with broken bones and the medical evidence says it is not explained by some health condition. In terms of the legislation, if the child is at risk of serious harm then you have to remove it."

Henaghan said the original family court judge, Judge Coyle, "agonised terribly" about the decision.

Chris Harvey, CYF southern regional director, said it had been an "incredibly complex case with conflicting medical evidence.

The original decision to place this baby in the care of wider family was made by the Family Court after considering the medical evidence and the opinions of various specialists."