Mason Lee was found dead in a Caboolture home on June 11, and his death made headlines after paramedics and police were seen sobbing in the street afterwards.
On Saturday, the Brisbane Times reported that two men, aged 35 and 17, and one 27-year-old woman are facing charges in relation to Mason's death.
According to Nine News, Mason's mother's boyfriend at the time of the crime, Andrew Sullivan, was among those arrested.
According to The Brisbane Times, Police Detective Inspector Paul Schmidt told reporters outside court that police believed that Mason died from peritonitis, a blood infection caused after the toddler's abdomen swelled when his small intestine ruptured.
"The injuries to the child would have been obvious, would have been deteriorating and would have been significant over a period of time," the senior detective told The Brisbane Times.
"Police will allege that the three people charged with manslaughter would have been in a position to know that he was medically unwell, required medical attention and failed to provide reasonable medical care."
It has previously been reported that child safety departments were aware of Mason Lee. Three months before his death, doctors notified child safety officials after he was admitted to hospital with a broken leg, severe nappy rash and ruptured bowel - injuries which suggested long-term abuse.
Health Minister Cameron Dick says doctors followed the correct procedures from their end. However, an investigation is now looking into why, despite this, Mason was returned to his family.