Paramedics rushed the 11-year-old to hospital with gunshot wounds to his face and neck from a unit in Sydney's Hills District on Monday, and on Thursday night police were told he had died from his injuries.
Police said they were met at the unit in Norwest by the victim, four 18-year-old men and a 44-year-old woman.
Three men were arrested before one was charged with concealing a serious indictable offence and two were released pending further inquiries.
The boy's school in Sydney's western suburbs said it was "deeply saddened" by the death of the Year 6 student.
In a statement, the school said it was supporting the boy's family and providing counselling services for students and staff.
The boy's father also paid tribute to his son, commenting "RIP my baby" on a social media post.
Several witnesses are believed to have been at the unit at the time of the shooting, and police were investigating possible organised crime links among those present.
''A number of individuals that were inside the unit at the time are well known to NSW Police and their association with organised crime is being considered,'' Superintendent Naomi Moore said on Tuesday.
''We do not know, and we are not eliminating any possibility about how this tragic situation happened.''
Investigations have so far failed to turn up a weapon.
Speaking to media on Friday, Police Minister Yasmin Catley offered her condolences to the boys parents.
"A young boy having access to a gun in the house is shocking, and that is why we want to take guns off the streets," she said.
She said a thorough investigation was underway, with the "best detectives" on the case.
Police Commissioner Mal Lanyon said any incident where a young person was killed was "tragic".
"It's difficult for the community. It's certainly difficult for first responders," he told reporters on Friday.
In response to questioning on Tuesday, Supt Moore said she would not suggest there was a ''gunman, so to speak'' that police were looking for.
The nature of the gathering in the unit remains a line of police inquiry.
The two men arrested and released might still face further police scrutiny.
The man charged with concealing an indictable offence faced court on Tuesday and will remain behind bars until his case returns to court in October.
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