A Japanese high court ruled Thursday that denying same-sex marriage is unconstitutional and called for urgent government action to address the lack of any law allowing for such unions.
The court does not have the power to overturn the current marriage law, which has been interpreted to restrict marriage as between a man and a woman. Government offices may continue to deny marriage status to same-sex couples unless the existing law is revised to include LGBTQ+ couples, or a new law is enacted that allows for other types of unions.
I believe this is because Japan works under a civil law system, which means that case law is subordinate to written law. This means that courts have much less power to impose their decisions upon the executive. Thus I think it is because the Japanese legislature never passed a law which explicitly allows for same sex marriage, the executive is allowed to deny these unions.
However this is based on a very surface level understanding of legal systems and I am by no means an expert. I find the language surrounding legal systems to be very confusing.