The owner noticed the bun was damaged as the woman was leaving the shop on Monday, and asked the woman to pay for the bread, police said.
When the woman refused, the manager followed her for 1km (0.6m) before restraining her, before police were called to the scene and the woman was arrested.
The store’s owner said they have seen the woman squash buns in their shop in Fukuoka before.
The 40-year-old was accused of being a serial bun-squasher by the store’s owner, who told police she had seen the woman do it before.
A woman in Japan has been arrested on criminal damage accusations after allegedly squashing a cream cheese bun in a supermarket.