Aerial footage on public broadcaster NHK showed grey smoke pouring from a concrete building in the city of Saitama, 25 kilometres (15 miles) north of Tokyo, as dozens of firefighters battled the blaze.
It took about five hours to extinguish the fire.
"A man who appeared to be in his 40s and two women who appeared to be in their 20s died after being sent to a hospital," a police spokesman told AFP.
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"We also found a body whose gender is undetermined inside the establishment," he added.
The seven people were slightly injured and treated in hospital.
The emergency services received calls from people inside the establishment saying they could not escape because the building was filled with smoke, according to NHK.
Police are investigating what caused the fire and the identity of the people who died.
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