He had only been in his role about 18 months but should have voiced those concerns at the time, the officer said.
The second part of a two-part inquest into the child's death began this week in the Wellington District Court before Coroner Marcus Elliott.
All involved in the case, including those giving evidence at the inquest, have name suppression, including the child, his mother and her partner.
The first part of the inquest last year found that the mother's partner, who died in custody weeks after he was charged with murdering the child, was responsible for the little boy's death.
The man's previous bail conditions were not to associate with children under 16 unsupervised. He was on release conditions for threatening speech.
Witness evidence to the inquest was that he had an extensive criminal history, including 19 convictions for violent offending, and wasn't allowed to have custody of his own children.
The toddler died days after he was discharged from hospital, with injuries considered suspicious by police.
This week's inquest will cover the systemic failings that led to the child being in the man's care, with witnesses from police, Oranga Tamariki, Corrections and the former District Health Board.
It would also explore the changes that have been made since the boy's death and identify any systemic issues that needed addressing.
The boy was found unresponsive in his bed by his mother. She had been at work the night before and not checked in on him when she returned that evening.
He could not be revived and was pronounced dead shortly after, having suffered from a fatal spinal cord injury caused by hyperflexion.
He had been in the care of the man, his mother's partner, the day before.
A pathologist described the little boy's injuries at last year's inquest as "uncommon" and the fractures would have taken extreme force to inflict.
Days before his death the child was seen by a number of doctors for a leg fracture, missing tooth, black fingernails and bruising.
Despite these injuries the boy was discharged home.
Discussions between Oranga Tamariki, doctors and police occurred to ascertain if it was appropriate to return the boy to his mother's care.
It was not known by authorities at the time that the woman's partner was helping with childcare while she worked.
The probation officer said he was concerned about how a social worker conducted the interview to determine if the man was suitable to live with children.
"Yes I had concerns with the way she spoke – I wasn't there to tell her how to do her interview," he said.
He described the man as an "angry one", and was surprised that a report presented by Oranga Tamariki said he had no concerns and described the man as exemplary.
"I did have real concerns about his risk and would not have said otherwise," he said.
Police witnesses said there was to be a "multi-agency safety management plan" to be put in place before the child's return home from hospital days before his death.
If there was access to reports about healing injuries before the child's death, police would have approached their investigation differently, according to police witnesses.
"Any healing injuries would have been a full stop to me," one witness said.
"Old healing injuries ... that is just a major red flag to me that something is not right in that household and the child is at risk."
According to police information at the time, the child wasn't in the care of the man at all and the missing tooth and black nails were explained by his mother to be from an accident at kindergarten and fingers caught in doors.
Since the child's death, there has been a "significant change in the family harm environment" according to police evidence, with staff and resourcing increasing tenfold.
At the inquest last year, it was heard the man said he had fallen on the child but thought he was fine.
Before admitting to "falling" on the toddler, he had denied any harm accidental or otherwise.
A pathologist had previously said it was unlikely the extensive injuries were caused by a fall.
Coroner Elliott said the boy died before his mother arrived home the evening before he was found unresponsive.
"I have reached the conclusion on the balance of probabilities that [the partner] intentionally inflicted the injuries which caused [the toddler's] death. However ... this does not amount to a finding that [he] murdered [the boy]."
The inquest is set down for four days.
