The gunman who assassinated Shinzo Abe targeted him because he believed the former Japanese prime minister had an association with a particular organisation, not because of his politics.

Japanese police said Tetsuya Yamagami, a 41-year-old arrested at the scene, held a grudge against this particular, perhaps religious organisation but have yet to confirm if it actually exists. Yamagami was undergoing mental health assessments police said.

“It’s not a grudge against the political beliefs of former Prime Minister Abe,” Nara police told reporters.

Flowers, bottles of water and a framed photograph of former Japanese prime minister Shinzo Abe rest in a makeshift shrine near the crime scene in Nara on Saturday.Credit:Bloomberg

Police found other homemade weapons and explosives at Yamagami’s apartment on Friday along with a computer and books. Yamagami told police that he had taken sick leave from his job at a manufacturing company in April and had been unemployed since May.

The Mainichi newspaper reported co-workers describing him as quiet, with no outspoken political beliefs of his own. The former Japanese maritime self-defence force member found out from an election campaign website on Friday that Abe was due to speak outside the Yamato-Saidaiji train station in the city of Nara.

Police said a man arrested at the scene and identified as Tetsuya Yamagami shot Abe while the former leader was delivering a speech. Credit:AFP

Yamagami shot Abe twice with a handmade gun, hitting the country’s longest-serving prime minister in the neck at 11.30am, Nara time. A second bullet became lodged in Abe’s chest near the wall of his heart.

Doctors at Nara Medical University Hospital tried frantically to save the 67-year-old but he was pronounced dead at 5.03pm just after his wife Akie arrived at the hospital. Akie accompanied Abe’s body back to Tokyo in a hearse on Saturday. A vigil is expected to be held on Monday after Sunday’s upper house election, and the funeral on Tuesday.

Former Prime Minister Shinzo Abe makes a street speech before being shot in front of a train station in Nara. Credit:Getty

Prime Minister Fumio Kishida vowed to continue with the upper house elections, saying he would beef up security to ensure voters and candidates could safely get to the polls. Reuters reported a metal detector had already been set up at the site of Kishida’s stump speech in a city south-west of Tokyo, an unusual security measure in Japan, along with increased police presence.

Toshimitsu Motegi, secretary-general of the Liberal Democratic Party, said the ballot had to go on “to show that we will not succumb to violence”.

At the site of the assassination on Saturday hundreds of mourners lined up at a makeshift shrine to lay flowers and pay tribute to Abe, the most influential Japanese politician of his generation.

A man prays at a site outside of Yamato-Saidaiji Station where Japan’s former prime minister Shinzo Abe was shot.Credit:Getty Images

“I’m just shocked that this kind of thing happened in Nara,” Natsumi Niwa, a 50-year-old housewife, told Reuters as she and her 10-year-old son laid flowers.

The architect of the 2012 economics policy that became known as Abenomics had inspired the name of her son, Masakuni, with his rallying cry of Japan as a “beautiful nation”, Niwa said. Kuni means nation in Japanese.

Abe was still a pivotal figure in the ruling LDP at the time of the attack. He controlled the party’s largest faction and the political fortunes of his successors Yoshihide Suga and Kishida.

A hearse carrying the body of former prime minister Shinzo Abe, arrives at his home in Tokyo on Saturday.Credit:AP

Residents also lined up outside Abe’s home in Tokyo as world leaders paid their respects. Abe founded the Japan, Australia, India and US group known as the Quad, drove the Trans-Pacific Partnership and spent more than a decade attempting to change his country’s pacifist constitution.

Sean King, an affiliated scholar at the University of Notre Dame’s Liu Institute for Asia and Asian Affairs said Abe’s death has left a void in Japan, the region and around the world “that won’t be filled anytime soon”.

US President Joe Biden said he was “stunned, outraged, and deeply saddened by the news”.

“We know that violent attacks are never acceptable and that gun violence always leaves a deep scar on the communities that are affected by it,” he said. Flags were ordered to fly at half-mast across the US.

Prime Minister Anthony Albanese said the Sydney Opera House would be lit up in the colours of the Japanese flag. Victorian Premier Daniel Andrews said landmarks across Melbourne would be covered in red and white to honour Abe.

Chinese President Xi Jinping offered condolences to Kishida on Saturday and said Abe had made contributions to help improve relations between the two countries, state-run broadcaster CCTV reported.

The statesman managed to keep a dialogue open with Beijing despite enraging Chinese nationalists with his visit to the Yakasuni Shrine – a memorial that includes Japanese officers who committed war crimes against Chinese villagers in World War II. Abe later led a rethink of Japanese policy towards China, particularly on Taiwan, which Tokyo came to view as a critical threat to its own security.

Chinese nationalists on Weibo labelled Yamagami “a hero” while jingoistic state tabloid The Global Times suggested the assassination would be used as an excuse to bolster right-wing and anti-China politics in Japan.

China’s Foreign Ministry said on Friday it was “shocked by the unexpected incident”. “Former prime minister Shinzo Abe had contributed to the improvement and growth of China-Japan relations,” said spokesman Zhao Lijian.

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