Police and firefighters inspect the site near Takeshita Street in Tokyo, early Tuesday.
Police say the man is suspected of intentionally trying to kill people by ploughing the medium-sized van into crowds who had lined the streets to welcome in 2019.
Eight New Year's revellers have been left injured after a minivan driver slammed into pedestrians in downtown Tokyo.
A 21-year-old suspect, named as Kazuhiro Kusakabe, was arrested and being questioned, Tokyo Metropolitan Police said.
Japanese television showed a grey coloured vehicle that was badly damaged in the front and dozens of police officers at the scene.
The police also found a 20-liter tanks of kerosene in the auto, which Kusakabe said he planned to use to burn the vehicle, according to the police. Media reports added that he had initially planned to spread the kerosene around to start a fire, but had been unable to do so because of security restrictions.
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Investigators said Kusakabe told them he carried out the attack "in retaliation for an execution" and "would not make any excuse" for his actions.
But it was unclear whether he was making a statement against the death penalty in general or was targeting a specific execution.
British counter-terrorism police are investigating stabbings at Manchester Victoria train station that left three people injured, including a police officer, on New Year's Eve.
The incident happened in the tourist and shopping destination of Harajuku on Takeshita Street, which is close to the Meiji Shrine. In 2008, a man drove his vehicle into a crowd in the popular Akihabara electronic-shopping district, got off and went on a stabbing spree with a knife.
The blast, which destroyed 35 units, killed at least seven people and left hundreds homeless in freezing temperatures.