A federal police spokesman said three explosive devices were found at the teenager’s home in the city’s upmarket suburb of Greendale.
The suspect will appear in Melbourne Children’s Court on Monday on charges of terrorism. His identity cannot be revealed for legal reasons.
Australian Prime Minister Tony Abbott spoke to reporters in Darwin on Saturday.
“The tragic truth is that there are people amongst us, not very many, it’s true, but there are some people amongst us who would do us harm, and it’s vital that our police and security agencies be given all the support and all the resources that they need to do their job properly,” Abbott said.
The teen was arrested on Friday afternoon in a joint federal-state police operation at his home in the upmarket suburb of Greenvale where the explosive devices were found, Australian Federal Police Deputy Commissioner Mike Phelan said.
There were reports of other homes being searched in nearby suburbs.
“We’ve got to examine lot of material that was seized at the premises, sift through a lot of intelligence, we have to get the full picture so we may not know exactly where it was going to occur nor when it was exactly going to occur, but let me tell you something was going to happen,” Phelan told reporters.
He added: “As a result of the Victoria police and AFP interception yesterday, some Victorians are going to be alive because of it. Had we not intervened, there was a real threat of action being taken.”
Police had contained the plot and there was no further threat from the suspect or his colleagues to the people of Victoria, Phelan said.
The arrest comes weeks after five Australian teenagers were arrested on suspicion of plotting an attack ceremonies commemorating ANZAC Day.