The teenage father, charged with seriously assaulting his infant son in Western Australia's South West, was under state care at the time of the incident.

Police allege the 15-year-old father critically injured the 28-day-old baby at Bunbury Hospital on Saturday night.

The youth, who has had a troubled history, was left alone with his son as the 16-year-old mother went to heat up some food.

The Minister for Child Protection, Helen Morton, says no concerns had been raised about the teen's behaviour towards his baby prior to the incident.

She says the youth had unsupervised access to the infant from the day he was born.

The department's director general Terry Murphy says the teenager was not considered a risk.

"This was not predictable," he said.

"It also needs to be said equally as bluntly, we do not know what occurred.

"This will unfold over time but at this time we do not know the cause of the injuries."

The Opposition's Stephen Dawson says it raises serious questions.

"I want to know why was this young boy left alone with this child and how did this happen?"

Ms Morton has ordered an investigation into the incident.

"It's really terrible for that baby, it's terrible for his young 16-year-old mum and her extended family, it's terrible for the young 15-year-old dad, and all the people that have worked with that young family," she said.

"It's just a really terrible, distressing situation."

She says her department has been supporting the family and the father before the child's birth.

"The involvement has been supporting that young family right through since the birth of the baby and even prior to that involved in the young dad, as a child in the care of the state," she said.

Ms Morton says the baby has been provisionally taken into the care of the department which will now make all future medical decisions on his behalf.

The child remains on life support at Princess Margaret Hospital in Perth.

The teenage father has been remanded in custody until he is due to appear in court again next week.