The city of Iga, Mie Prefecture, will start recognizing same-sex partnerships as equivalent to marriage in April, becoming the third local government to address discrimination against sexual minorities.
The certificates will be issued starting April 1. Tokyo's Shibuya and Setagaya wards introduced similar systems last year.
Same-sex marriages are not legal in Japan, and couples often face difficulties when seeking housing or making hospital visits to their partners because they are not considered family.
"It is a step forward to achieving a diverse society," Iga Mayor Sakae Okamoto said in a notice posted in front of City Hall.
"Addressing the human rights issue of LGBT people from a global perspective is very meaningful," Okamoto said, referring to lesbian, gay, bisexual and transgender people.
Couples living in Iga who are 20 or older can apply for the certificates but must first submit official paperwork documenting whether they have taken a partnership oath. The mayor will then issue the certificates, the city said.
Iga is better known as home to the Iga ninja clan and holds the Iga Ueno Ninja Festa each year.