Isaac Bechara, now 19, was one of 10 people inside a property in Sydney's Hills District when he allegedly shot the boy on September 21.
The 12-year-old was treated at the scene in Norwest before being rushed to hospital with gunshot wounds to his face and neck.
He died three days later.
Bechara, who turned 19 in the weeks since the incident, was on Tuesday charged with murder at a Silverwater correctional centre.
He had been in custody since being charged with concealing a serious indictable offence soon after the shooting.
Despite the murder charge, homicide detectives are unclear whether the shooting was deliberate.
"There is no evidence at this stage to show that it was a deliberate shooting, or it was an accidental shooting," NSW Police Detective Superintendent Joe Doueihi told reporters on Wednesday.
"We rely on the fact it was dangerous and reckless."
Det Insp Doueihi stressed there was no evidence the 12-year-old shot himself or that he had handled the firearm at any point.
"We are clearly alleging the 19-year-old male is responsible for this tragic death," he said.
Central to the ongoing investigation is the search for the handgun allegedly used by Bechara, which remains missing.
Police believe it may have belonged to a friend of the victim's brother, who is alleged to be involved with organised crime.
Det Supt Doueihi said those inside the unit at the time had given a version of events, but its truthfulness was dubious.
"I don't believe they've been entirely truthful with us," he said, adding the boy's mother and brother had cooperated with investigators.
Bechara was one of three men arrested soon after the shooting.
The other two, both also 18 at the time, were released pending further inquiries.
Det Supt Doueihi said Bechara was not known to police beyond a previous conviction for affray, for which he was serving an intensive correction order.
His lawyer, Jeresyn Legal's Joe Nasr, did not apply for bail when Bechara's case was heard in court on Wednesday.
Bechara is expected to appear at Parramatta Local Court on Thursday, before fronting Downing Centre Local Court in December.
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