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+They are designed to encourage landlords and hospitals to treat gay couples the same way as married ones.
+BBC Tokyo correspondent Rupert Wingfield-Hayes says campaigners are welcoming "a small step forward in a deeply conservative country".
+Younger people in Japan generally support gay rights but the prime minister has previously urged caution over changing the law.
+Hiroko Masuhara, 37, and Koyuki Higashi, 30, were the first to register their partnership in Shibuya district.
+Ms Higashi, an actress, told reporters she hoped the measure would spread across Japan and eventually lead to same-sex marriage being legalised.
+Japan does not have any national legislation specifically banning discrimination against gay people. Couples complain of being blocked from tenancies and prevented from visiting loved ones in hospital.
+"I hope the day will come soon when there will be equality in society," Ms Higashi said, according to the AFP news agency.
+Setagaya's mayor Nobuto Hosaka issued five same-sex couples with the papers on Thursday afternoon, according to the Kyodo news agency.