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A no trespassing sign outside the entrance of the Family Federation for World Peace and Unification, more commonly known as the Unification Church, in Tokyo, on Aug. 29.KIM KYUNG-HOON/Reuters

More than three months after former Japanese leader Shinzo Abe was murdered by a man infuriated by his links to the Unification Church, Prime Minister Fumio Kishida has ordered an official probe into the religious group’s ties to his ruling Liberal Democratic Party.

About half of LDP lawmakers have disclosed connections to the church in recent months, many after initially denying any such links, and the scandal has seen Mr. Kishida’s popularity plummet. A poll last week showed support for his government had dropped below 30 per cent for the first time, while the Prime Minister’s personal approval rating is frequently in the low 20s.

His decision to hold a state funeral for Mr. Abe last month amid the revelations sparked protests and exacerbated his unpopularity. Speaking to parliament Monday, he apologized on behalf of the LDP – which has been in power since 2012 and has run Japan for most of the past six decades – and said the scandal has undermined trust in government.

He instructed his Culture Minister to prepare an investigation into the church under the Religious Corporations Act, saying he was “taking seriously” allegations that the church has left many followers impoverished and has disrupted their families.

That was what Mr. Abe’s assassin, Tetsuya Yamagami, claimed had happened in his case. He told police his mother had been bankrupted by the church through frequent demands for donations and blamed it for the breakdown in their relationship.

Former members of the church have long accused it of aggressive “spiritual sales” practices, including cajoling members into selling goods door to door at exorbitant prices or making large donations to the church. According to Japan’s National Network of Lawyers Against Spiritual Sales, “many families have been driven to collapse” by the practices, which it estimates have raked in 123 billion yen ($1.1-billion) for the church since the 1980s.

The Unification Church – officially the Family Federation for World Peace and Unification – has stridently denied such claims and called the figures released by the lawyers’ group “inaccurate and unfair.”

Founded by South Korean pastor Sun Myung Moon in 1954, the church claims about 10 million followers globally, with some 600,000 in Japan, a country of more than 125 million people. Its Japanese offices are in a nondescript, three-storey building tucked down a side street in Shibuya, a busy shopping district in Tokyo.

But the group’s apparently modest footprint belies its outsized political influence. Beginning in the 1960s, the stridently anti-communist church cultivated ties with the LDP, including with Mr. Abe’s grandfather and father, both former prime ministers. According to former members, followers were told who to vote for at election time and provided free canvassing and other support for LDP candidates.

There are dozens of Unification Church ministries across Japan, and the organization has significant investments in media, schools, ginseng production, real estate and fishing operations. Donations from Japan are a major source of revenue for the global church, which is headquartered in the United States and now run by Mr. Moon’s widow, Hak Ja Han.

Kwak Chung-hwan, a former church official, told Reuters that Japanese followers were treated like “an economic army” by the group. Hiroshi Yamaguchi, a member of the National Network of Lawyers Against Spiritual Sales, said that before Mr. Abe’s assassination the church brought in about 10 billion yen ($93-million) a year from Japan. The church has denied these claims.

In recent months, the Unification Church has hemorrhaged members and political support. The Japanese media, which for decades largely ignored the LDP’s links to the organization – which were not kept secret – is now focused intensely on the stories of former members and claims of abuse.

“They are definitely under siege from the media,” said Jeffrey Hall, a special lecturer in Japanese studies at the Kanda University of International Studies in Chiba. “The church will be very badly damaged by this scandal. They’ll lose their friends in government and have a very, very hard time ever recruiting new members. And their fundraising in Japan will be harmed significantly.”

Last month, the church established a new office for promoting reform and has vowed to stamp out aggressive sales and donation practices. It has also filed a lawsuit against some Japanese media for airing what it said were unfounded accusations and tried unsuccessfully to stop a news conference at the Foreign Correspondents’ Club of Japan this month by a second-generation former member.

At that event, a woman using the pseudonym Sayuri Ogawa said both her parents were active members of the church and had donated a total of 10 million yen ($90,000) to the group over the past 40 years. Ms. Ogawa said her parents also forced her to donate almost two million yen of her own money.

“I was supposedly cherished as a child of God at church, but there was a huge discrepancy between that and my real life,” she said, adding that her family was impoverished as a result and that she had been sexually abused at a church retreat. “There are many other victims like me who are suffering.”

Church officials have pushed back, claiming their followers are being harassed and victimized. Speaking at a news conference, church president Tomihiro Tanaka said, “Our members in Japan have been subjected to death threats, abusive language and obstruction of assemblies.”

The church in Japan may not survive the scandal. A panel of experts advising the government said in a proposal Monday that dissolving the church should be an option.

Only two other organizations have been dissolved under the Religious Corporations Act: the doomsday Aum Shinrikyo cult, which carried out the 1995 sarin gas attack on the Tokyo subway, and the Myokakuji temple group, which was accused of defrauding members.

Aum Shinrikyo – whose leader, Shoko Asahara, was executed in 2018 along with 12 other members – regrouped under the name Aleph and continues to operate today, albeit under tight government scrutiny.

Mr. Hall said such an option might be difficult with the Unification Church, which has already reinvented itself several times.

“Even if they change their name, that will be big news,” he said. But the group should not be counted out just yet.

“They might just hunker down and portray themselves as victims of an unfair media and left-wing lawyers. There’s still a chance they could have political influence in the future, because it’s no small thing to throw away 50,000 or 70,000 votes, and they’ll be useful to somebody, because a religious voting bloc is far more reliable than just normal conservative voters.”

With files from Reuters.