The ordinance in this regard, approved by the local assembly, will take effect on Wednesday and will permit the district to issue certificates to same-sex couples, an important step in the country where civil law does not recognise same-sex marriages, Efe news agency reported.
These certificates, however, will recognise same-sex partnerships as different from marriage, and will have no legal force.
Nonetheless, the legislation includes measures to ensure that same-sex unions are granted a status similar to that of marriage with regard to tax benefits, social security and the right to jointly own property.
The decision has been celebrated by gay rights advocates and politicians supporting the issue, but has also been criticised by both conservative camps and the Japanese government.
Japanese state news agency Kyodo quoted Sadakazu Tanigaki, secretary-general of the ruling Liberal Democratic Party, as saying that the initiative “could affect the foundations of the social system” of the country.
Japanese Prime Minister Shinzo Abe has been reluctant to legalise same-sex marriage.
In an address to parliament, Abe asked for “cautious consideration” of the matter, saying it “concerns the foundation of how families in our country should be”.
Other Tokyo districts, such as Setagaya, have also begun the process of approving same-sex unions.