The man said he instead spent the night under an umbrella beneath the eaves of a building.
"I want them to allow me into the facility because the wind was strong and it was raining," he said.
Another homeless man was turned away later afternoon.
What was the reaction?
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."