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.
Prime Minister Shinzo Abe was asked about the case in parliament and said "evacuation centres should let anyone in who has come to evacuate".
"We will look into the facts and take appropriate measures," he added.
The Taito ward said it would review its procedures to help people without addresses in the ward.