Police are investigating whether the blaze was started deliberately, public broadcaster NHK said.
The victims suffered cardiopulmonary arrest, a term often used in preliminary reports before a death is officially confirmed, reports say.
Footage showed blackened windows after dozens of firefighters extinguished the blaze on the fourth floor.
All of those feared dead were reportedly in a psychiatric clinic on the fourth floor of the building, located in a busy commercial and entertainment district.
Emergency services were alerted shortly after 10am local time on Friday.
"There was lots of dark smoke," one eyewitness told NHK, adding: "There was a very strong smell, too."
Another witness said she saw a woman in the building calling for help.
"When I looked outside I saw orange flames at the fourth-floor window," she told Kyodo News. "A woman was waving her hands for help from the sixth floor."
Some people were evacuated from the building by fire crews using ladders.
The blaze was successfully extinguished within half an hour, after it burned across an area of approximately 20sqm, the local fire department said.
No damage has been reported to other floors within the building or any neighbouring properties.
Last year, Japan saw one of its worst mass casualty incidents since World War II after a man set fire to a film studio in Kyoto in 2019, killing 36 people.