The boy was found in a vehicle after what police believe was an attempt to flee the site of a firebombing in Taylors Hill, northwest Melbourne, on Monday.
On Thursday, police arrested two 16-year-old boys and a 15 year-old boy for questioning over the incident.
Emergency services responded to reports of two cars set alight on Woolwich Way in Taylors Hill, shortly after 5am on Monday.
Officers arrived to find the vehicles engulfed in flames and the severely burned 13-year-old boy nearby.
Police believe he attempted to flee in a vehicle before crashing into bushes.
The boy remains in hospital in a critical condition.
Arson and Explosives Squad Detective Inspector Chris Murray said police were committed to finding others involved in the arson and holding them responsible for the teen's injuries.
"We have a young boy whose life is currently hanging in the balance," he said.
"Let me be clear: this is not a game – no amount of money is worth risking your future or your life. Lighting a fire means putting yourself in danger."
Criminal syndicates were tasking youth people with committing crimes for them because they viewed them as easy to manipulate and replace, according to Det Insp Murray.
"They are the ones who profit, whilst young offenders bear all the risk," he said.
Victoria has experienced a spate of arson attacks on vehicles, homes and businesses which police believe is linked to organised crime.
Young people may be recruited online or over encrypted apps to carry out crimes on behalf of criminal syndicates.
"We are seeing arson being used as a means to intimidate and affect people generally within the organised crime areas across Victoria," Acting Commander Troy Papworth said
Why criminals were increasingly choosing arson as their chosen means of intimidation or revenge was "a really good question", he said.
"We as police observe trends; so do those involved in organised crime," he told reporters on Thursday.
"The means to commit arson are very readily available.
"It's not illegal to be carrying a box of matches. It's not illegal to have a can of fuel and be driving around with it."
In July, police launched Operation Phoenix to increase late night patrols targeting those either on the way to or from committing a crime, which has resulted in 165 arrests.
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