Justice Minister Yoshihisa Furukawa said Tomohiro Kato had undertaken “meticulous preparation” for the attack and had shown a “strong intent” to kill.
“The death sentence in this case was finalised through sufficient deliberation in court,” he told reporters.
“Based on this fact, I approved the execution after extremely thorough scrutiny.”
The June 2008 attack, which also injured 10 people, began with Kato driving a truck into a crowd. After stabbing several people, the then 25-year-old was arrested at the scene, telling police: “I came to Akihabara to kill people. It didn’t matter who I’d kill.”
Police said he documented his journey to Akihabara on internet bulletin boards, typing messages on a mobile phone from behind the wheel of the truck and complaining of his unstable job and loneliness.
The son of a banker, Kato grew up in Aomori prefecture in Japan’s north, where he graduated from a top high school. He failed his university entrance exams and eventually trained as a car mechanic, reports said.
Prosecutors said Kato’s self-confidence had plummeted after a woman he had chatted with online abruptly stopped emailing him after he sent her a photograph of himself.
His anger against the general public grew when his online comments, including his plans for a killing spree, drew no reaction, prosecutors said.
The victims “were enjoying their lives, and they had dreams, bright futures, warm families, lovers, friends and colleagues,” Kato wrote according to a copy published in the Shukan Asahi weekly.
The use of the death penalty in Japan is shrouded in secrecy. Those on death row might only find out the sentence will be carried out a few hours before or sometimes not at all, while their families are usually only notified afterwards, according to Amnesty International.
Amnesty, which is opposed to the death penalty in all cases, says the general trend around the world remains towards the abolition of capital punishment.