The death of the boy, identified as Makai, is being led by task force Prime, set up last month to probe suspected neglect in the death of a six-year-old girl named Charlie.
Mr Stevens said detectives had significant material to work through and would be speaking to a number of witnesses.
He said because of the nature of a criminal neglect charge, it would take time to determine if the threshold had been met.
"We start from the premise that the circumstances that we're aware of give rise to a concern that criminal neglect may be a situation that needs to be identified," the commissioner told reporters on Tuesday.
"The work is done now to establish all of the information, all of the facts and compile the evidence.
"I'd be reasonably confident we'd (also) be seeking an opinion from the director of public prosecutions before we proceed."
In conjunction with the police investigation, former SA police commissioner Mal Hyde has been engaged to lead a review into how government agencies, including child protection, handled the cases involving the two children.
That review was initially placed in the hands of the chief executive of the Department of Premier and Cabinet but with news that a second death was under investigation, Premier Peter Malinauskas said it had been decided to ensure it was completely independent of government.
"This is about making sure we have a review of integrity, of independence and robustness so we fully understand what interactions occurred between government agencies and these families," the premier said.
"To see whether or not there were failures of systems that could be addressed and should be addressed."
Mr Malinauskas said Mr Hyde's report would be made public.
Revealing details of the boy's death on Monday, Detective Superintendent Des Bray said the child was taken to Adelaide's Lyell McEwin Hospital in February this year and later transferred to the Women's and Children's Hospital, but died the same day.
A post-mortem examination identified several serious health issues, but initially they were not considered suspicious.
"The provisional cause of death, although it was unusual because you don't expect children to die, was not cause for immediate concern," Supt Bray said.
The boy's death was reviewed in accordance with usual coronial procedures, and when further information was obtained from child protection authorities and an opinion provided by a paediatric expert, police formed the view a criminal investigation was warranted.
Mr Stevens said while there was a level of detachment when provided with a brief in any case, once the circumstances were known and a name and face were put to the victim, "it certainly has a more significant impact on you".
"The death of any child is devastating. For a criminal investigation to result from that death is quite disturbing," he said.
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