Three same-sex couples' claims were denied by a district court in western Japan's Osaka as part of a series of lawsuits brought by activists demanding marriage equality.
The court judgement stated, "From the perspective of individual dignity, it is vital to realise the benefits of same-sex couples being publicly recognised through official recognition."
The judgement went on to clarify that the current refusal to recognise such unions "is not regarded to be a violation of the constitution," and that "public debate on what kind of system is appropriate for this has not been adequately carried out."
The lawyer for the plaintiffs in the case, Akiyoshi Miwa, said he was "shocked" by the court's refusal to intervene in the dispute.
"It suggests the judge is stating the court is not need to actively engage in human rights matters," Miwa explained.
Machi Sakata, who married her American spouse in the state of Oregon in the United States, said she "couldn't believe the verdict."
The court also found that same-sex partners might get legal privileges if a structure akin to marriage was adopted.
"Nothing can take the place of you" (marriage). I'm filled with resentment. "It's as if they're saying, 'We don't treat you fairly, but that's OK, right?'" Sakata explained.
Last year, a district court in northern Sapporo ruled the contrary, saying that the government's refusal to allow same-sex marriage was a violation of the constitution's promise of equality under the law.
Campaigners hailed the decision as a huge win that would put pressure on politicians to recognise same-sex unions.
"Marriage shall be solely with the mutual consent of both sexes," the Japanese constitution states.
Local governments around the country have begun to recognise same-sex partnerships in recent years, while such recognition does not provide the same legal privileges as marriage.
Last month, the Tokyo prefecture said that it would begin recognising same-sex unions in November, amending existing legislation.
In 2020, more than a dozen couples filed lawsuits in district courts around Japan demanding marital equality. The synchronised effort, they said, was meant to put pressure on the sole G7 country that does not recognise gay unions.
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