Mourners lined the streets of central Tokyo on Tuesday to bid farewell to assassinated former Japanese prime minister Shinzo Abe, as his hearse was driven past political landmarks after a private funeral.

The country's longest-serving prime minister was gunned down on Friday while campaigning, in a crime that rattled Japan and prompted an outpouring of international condemnation and grief.

His funeral was held at Tokyo's Zojoji temple on Tuesday, with relatives and close acquaintances in attendance.

But elsewhere in the temple compound, thousands of well-wishers lined up in the humid heat to pay their respects before a photo of the late leader, who held office until 2020.

"I can't get over my sadness, so I came here to lay flowers and say a prayer," consultant Tsukasa Yokawa, 41, said, describing Abe as "a great prime minister who did a lot to elevate Japan's presence" on the global stage.

After the service, a hearse carrying Abe's body departed for a final tour of some of the political landmarks he served in throughout his career: the parliament, prime minister's office, and headquarters of his ruling Liberal Democratic Party.

Outside each, staff and officials including ministers and senior LDP figures stood sombrely. They pressed their hands together and bowed their heads in respect as the car arrived.

Abe's widow Akie sat in the front of the hearse, carrying her husband's mortuary tablet inscribed with his posthumous Buddhist name, and bowed back.

Along the route from the temple to the site, residents gathered to offer prayers and take photographs of the former leader's last procession.

Abe was campaigning in the western city of Nara when he was shot.

The murder suspect, 41-year-old Tetsuya Yamagami, is in custody and has told police he targeted Abe because he believed the politician was linked to an organisation he resented. (AFP)