As news spread on social media, there was outrage at the shelter's decision.
"Is this a country that's going to host the Olympics in Tokyo? [in 2020]" asked one Twitter user. "People from abroad would see this and think this is a terrible country."
The San'ya Workers' Welfare Centre, a charity, responding by opening as a shelter on Saturday night.
But others were less sympathetic, suggesting "smelly" or "mentally ill" homeless people should only be allowed into shelters if there was a separate space.
"If you claim your rights, do your duties first," said one Twitter user. "Can you sleep next to a stinking person?" asked another.