The recall comes about a week after the company first started asking retailers to pull the products from shelves, saying some cups were "swelling and bloating." Chobani had previously said it wasn't issuing a formal recall.
But the Food and Drug Administration said Wednesday that it was in talks with the company about the matter.
Chobani said that most of the affected products have already been pulled from shelves. The company, based in New Berlin, N.Y., said the affected products came from its Idaho facility and represents less than 5 percent of its total production.
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. He said the problem was caused by a type of mold that is commonly found in dairy environments. The issue has been "totally fixed," he said, noting that the mold became a problem because Chobani doesn't use preservatives in its products.
Ulukaya did not say exactly how many reports of illnesses the company received, but said it was not in the hundreds or thousands.
"Everybody in the company took this hard," Ulukaya said. "It shook us up."
This week, the company was responding online to customers who were complaining about their yogurt. One person said her yogurt was "unnervingly fizzy" and another said it tasted like "wine."
The affected products include a number of different size containers:
-- Chobani 6 ounce cups
-- Chobani 16 ounce tubs
-- Chobani 32 ounce tubs
-- Chobani 3.5 ounce cups
-- Chobani Bite 3.5 ounce cups
-- Chobani Flip 5.3 ounce containers