The assassination of Japan’s former prime minister, Shinzo Abe, resurrects Japanese complexes about the role of Koreans living in their midst — many of them Japanese citizens seemingly integrated fully into Japanese society, many more of them Korean “residents” of Japan who have retained their Korean citizenship.

The reason is that the Japanese man who allegedly shot Abe with his home-made rifle has told police he was outraged by Abe’s links to the Unification Church, a Korean organization with a worldwide membership, including about 300,000 followers in Japan and 200,000 in South Korea.

“It’s a conspiracy,” a Japanese woman avers, attributing the killing to a plot to win votes for the ruling Liberal-Democratic Party, which increased its grip in elections Sunday for the upper house of the Japanese diet. “The assassination won votes for the LDP.”

The logic may seem convoluted since Abe was a pillar of the LDP, and the current prime minister, Fumio Kishida, now leads the LDP, in power almost continuously since its founding in 1955. The alleged assassin, Tetsuya Yamagami, told police the church had pressured his mother to donate the family fortune to the church.

Now, Japanese accuse the Unification Church, founded in Korea by the Reverend Sun Myung Moon, of infiltrating the highest levels of the Japanese political system. Moon is now dead, but the accusation is that the infiltration began with Moon’s relationship with Abe’s grandfather, Nobusuke Kishi, Japan’s prime minister in the late 1950s.

The fear is that the assassination will fuel anti-Korean feelings in a country in which Koreans historically have been victims of prejudice that often relegated them to the lowest rungs of society in terms of jobs and living conditions. The numbers are somewhat elusive, but about 2 million people of Korean or mixed Korean Japanese ancestry live in Japan.

They include descendants of those who moved there in search of jobs while Japan ruled Korea, and thousands more who were forced to work in factories in Japan during World War II. “We like to think we’ve outgrown anti-Korean feelings,” one Japanese told me, “But they are not so far beneath the surface.”

 Japanese are forever mindful of what happened in panic after  the Great Japan Earthquake of 1923. Mobs, backed by police, killed several thousand ethnic Koreans blamed for starting fires as the ground shook in and around Tokyo for as long as 10 minutes, killing more than 140,000 people.

At the heart of the alliance between Kishi and Moon was the staunch anti-Communism of the Moonies, as members of the church came to be called, and the sense that Moon would uphold the conservatism of the LDP. That sense was passed from generation to generation as power shifted to Kishi’s younger brother, Eisaku Sato, prime minister between 1964 and 1972.

Shinzo Abe, Kishi’s maternal grandson, nurtured the relationship with the Unification Church during his first stint as prime minister, between 2006 and 2007, and then when he returned as prime minister for another eight years, between 2012 and 2020.

The editor of the Tokyo website Shingetsu News, Michael Penn, quotes a paper written by Richard Samuels in 2001 stating that the Unification Church “built its Japan headquarters on land in Tokyo once owned by Kishi.” Church members served as LDP campaign workers, he writes.

“In return,” he goes on, “for many years the Church enjoyed protection from prosecution by Japanese authorities for their often fraudulent and aggressive sales and conversion tactics.” Mr. Samuels is quoted as writing that “by the 1980s, Japan reportedly provided some four-fifths of Unification Church revenues worldwide.”

The Unification Church in Japan has acknowledged that Mr. Yamagami’s mother was a church member but denies she was milked for excessive donations. The church, highly sensitive to such claims and fearful of an anti-Korean reaction, almost immediately put out condolences over Abe’s death.

“The Family Federation for World Peace and Unification (commonly known as the “Unification Church”) would like to express our shock and grief over the assassination of the former Japanese Prime Minister Shinzo Abe,” the statement said. “Our thoughts and prayers are with his family in the wake of this tragedy.”

The statement described Abe as “a globally respected statesman” who “often spoke of the need to value freedom and democracy,” and condemned “this act of violence.” With a bow to Japan’s strict anti-gun laws, it said, “Guns have no place in our religious beliefs or practices.”