The father was granted interim name suppression today to protect his child's identity.
Court documents reveal the charge relates to the alleged harming of the baby girl between October 14 last year and February 18 this year - the day she was admitted to hospital with multiple injuries of various ages.
Police allege the child was hurt on multiple occasions in her first four months of life.
The injured baby's father was arrested and charged yesterday and was in custody overnight.
He appeared in court just after 4pm.
A number of family members were in the courtroom to support him.
He smiled at them from the dock, where he stood with his hands clasped in front of him.
The man was remanded on bail until April 18 and ordered to surrender his passport and have no contact with his daughter or her mother.
He is also not allowed any unsupervised contact with anyone under 16.
It was revealed in court that he has no previous convictions.
Earlier this month the Herald revealed the baby girl was injured over a period of time and when she was finally admitted to hospital she had fractures to her skull, arms, legs and ribs.
Police described the injuries as "significant" and, along with medical experts, believe they were not accidental and someone deliberately harmed her.
The baby's parents took her to their doctor on February 18.
The doctor, concerned at the state of the child, referred her to Middlemore Hospital where she was admitted.
There, medical staff established that she had 16 fractures of various ages - meaning the injuries were not inflicted during one incident.
"The fractures have been described by medical experts as being of varying ages and classically associated with non-accidental injury," Detective Sergeant Eddie Sutherland said last week.
Last week the Herald visited the house where the baby lived with her parents.
Family members of the baby refused to comment.
Had the man not been granted suppression this afternoon, the Herald still would not have been able to name him.
Under the Criminal Procedure Act, young victims who survive violent attacks or abuse cannot be named or identified, which means that as the accused is the baby's father, his name and image cannot legally be published.
The baby was taken into the care of Oranga Tamariki after she recovered enough to be discharged from hospital.
She - and her sister - remain in the agency's care.