No one knows exactly what happened when the 37-year-old man was alone with the child in regional Victoria on June 10, 2016.

But the infant was left with wrist, leg and skull fractures, as well as bleeding on and swelling of the brain.

Her father, who cannot be named to protect the child's identity, has been found guilty by a jury of intentionally causing serious injury.

County Court Judge Mark Taft said the 37-year-old's actions were "grave" and "reprehensible".

"A six-week-old baby has almost been killed," the judge said.

"You cannot imagine a more vulnerable position than that child.

"I have not encountered a worse case when serious injury has been imposed than that which is before this court."

Despite court documents saying the child is the man's biological child, he insists she is not and that his partner cheated on him while he was in prison.

He also denied assaulting the baby and tried to pin her injuries on his partner.

While it's unclear exactly what happened after the woman left to go shopping, prosecutors say her baby was choked, shaken and suffered blunt force trauma to the head.

It was possible the man "exploded with rage" after being woken by the child's cries or being unable to sleep because of his ice use, Judge Taft said.

The man has borderline personality disorder and a history of heroin, cocaine, cannabis and alcohol abuse following a traumatic childhood.

Before the incident, court documents show he lunged at his partner with a knife as she held their baby and in the presence of her other children.

The woman ran from the house yelling "help, help, he's going to kill me" as the man smashed up the house and threw the baby's bassinet.

She said her life fell apart after her partner shook their baby.

"Not knowing what or how this happened has stayed with me ever since," she told the court in a statement.

After the little girl was released from hospital into the care of a foster family, she did not make a sound for months.

"She didn't make a sound all the way home. For the first six months, she made no sound," the family said.

When the little girl, now three, asks about scars on her legs, her foster family says they make her run faster.

Judge Taft criticised steps taken by the Victorian Department of Health and Human Services to protect the woman and her family before the baby was injured.

The department arranged for the woman's brother and his partner to live with the family for protection.

"All of them used ice on a daily basis and it was a recipe for diaster," the judge said.

He will hand down his sentence at a later date.

Australian Associated Press