The church said it was considering an immediate appeal of the Tokyo District Court's revocation of its legal status on Tuesday, which would take away its tax-exempt privilege and require liquidation of its assets.
The order followed a request by Japan's education ministry in 2023 to dissolve the influential South Korea-based sect, citing manipulative fundraising and recruitment tactics that sowed fear among followers and harmed their families.
The Japanese branch of the church had criticised the request as a serious threat to religious freedom and the human rights of its followers.
The church called the court order regrettable and unjust and said the court's decision was based on "a wrong legal interpretation and absolutely unacceptable".
The investigation into Abe's assassination revealed decades of cosy ties between the South Korea-based church and Japan's governing Liberal Democratic Party.
The church obtained legal status as a religious organisation in Japan in the 1960s during an anti-communist movement supported by Abe's grandfather, former prime minister Nobusuke Kishi.
The man accused of killing Abe resented the church and blamed it for his family's financial troubles.
The church, which officially calls itself the Family Federation for World Peace and Unification - nicknamed "the Moonies" after its founder, the late Reverend Sung Myung Moon - is the first religious group subject to a revocation order under Japan's civil code.
Two earlier case involved criminal charges: the Aum Shinrikyo doomsday cult, which carried out a sarin nerve gas attack on the Tokyo subway system, and Myokakuji group, whose executives were convicted of fraud.
The church tried to steer its followers' decision making, using manipulative tactics, making them buy expensive goods and donate beyond their financial ability and causing fear and harm to them and their families, seriously deviating from the law on religious groups, officials and experts say.
The Agency for Cultural Affairs said the settlements reached in or outside court exceeded 20 billion yen ($A210 million) and involved more than 1500 people.
The church was founded in Seoul in 1954 by Moon, a self-proclaimed messiah who preached new interpretations of the Bible and conservative, family-oriented value systems.
The church faced accusations in the 1970s and 1980s of using devious recruitment tactics and brainwashing adherents into turning over huge portions of their salaries to Moon.
In Japan, the group has faced lawsuits for offering "spiritual merchandise" that allegedly caused members to buy expensive art and jewellery or sell their property to raise donations for the church.
The church has acknowledged excessive donations but says the problem has lessened since the group stepped up compliance in 2009.
