The discovery was made on the evening of Dec. 6.
An employee noticed what appeared to be a child's head while cleaning a refrigerator in the office and immediately notified the police at around 9 p.m. (local time), the Mainichi cited the police as saying.
Police subsequently searched the entire premises and found a severed head wrapped in a plastic bag inside the freezer compartment.
Below it, in a food container, police discovered two arms and two legs.
Initial assessments indicate the remains belonged to a child under one year old, and officials have not been able to determine the baby's gender, according to the Japan Times.
A 35-year-old man who works at a nearby restaurant told the newspaper that the venue is used as a waiting room for sex workers.