According to Japanese media outlet NHK, the company reported that the contamination took place at a restaurant in Tottori Prefecture on January 21.
The rat is believed to have entered one of several bowls being prepared for customers.
The company stated that the restaurant was immediately closed for inspection and reopened only after the local public health center completed its examination.
A staff member failed to inspect the bowls, resulting in the oversight. Sukiya has instructed all outlets to thoroughly check dishes before serving them.
The company issued an apology and pledged to strengthen its management system to prevent similar incidents in the future.