The move comes about a week after the company first started asking retailers to pull the products from shelves, saying some cups were "swelling and bloating."
Until now, Chobani had said it wasn't issuing a formal recall.
The compnay says the affected products came from its Idaho facility and represents less than 5 percent of its total production.
Chobani says most the affected products have already been pulled from shelves.
The containers are marked with the code 16-012 and expiration dates Sept. 11 to Oct. 7.
In an interview, Chobani CEO Hamid Ulukaya said it was the company's decision to move to a recall, not the FDA's. Ulukaya did not say exactly how many reports of illnesses the company received, but said it was not in the hundreds or thousands.
The company said on its blog that the problem was caused by a type of mold that is commonly found in dairy environments. The comany said the issue has been "totally fixed," adding that the mold became a problem because Chobani doesn't use preservatives in its products.
The company posted an apology from Ulukaya on its Facebook on Wednesday. In the post, Ulukaya offered his "heartfelt apologies" for the recall. He pointed affected customers to Chobani's Customer Loyalty Team.
The Associated Press contributed to this report.