The company revealed last week it had been using stale ingredients in a wide range of products and has now been forced to suspend sales in at least 31 retail outlets throughout Japan.
The scandal is the first of its kind in the new year but highlights a worrying pattern in the industry - coming just months after US chocolate maker Hershey recalled 21 products after discovering samples of salmonella. In a separate incident in the UK last summer, Cadbury Schweppes also faced a major product recall after waste water leaked salmonella bacteria into the chocolate crumb used to make several core brands.
Fujiya said it had used out-of-date eggs, cream and milk in manufacturing cream puffs and other items as well as shipping products before ensuring they passed bacterial tests.
According to local press, Fujiya president Rintaro Fujii and company executives admitted: "Our quality control capacity and response were inadequate." in a Tokyo press conference held earlier this week.
Fujii has since announced that he will step down as president and it is likely the company will face re-examination of its quality control certification.