The company said it has investigated and found a type of mould commonly found in dairy that may be to blame.
Chobani said the affected product came from its Idaho facility and represents less than 5 per cent of its total production. The company has been working with retailers to remove and replace containers with the code 16-012 and expiration dates Sept. 11 to Oct. 7.
Chobani, which is based in New Berlin, N.Y., did not say how many of its cups or what varieties were affected. The effort was voluntary and it is not issuing a formal recall.
A representative for Kroger, the nation's largest traditional supermarket operator, said Chobani issued a product withdrawal Friday. "It was not a food safety issue," Kroger spokesman Keith Dailey said in an email.
On Tuesday, Chobani was responding to people who were complaining about their yogurt cups on Twitter. One person described her cup as "unnervingly fizzy," another said the cups were like "yogurt soup" and another said it tasted like "wine."
Yet another person said the strawberry flavour they bought tasted "really old."
Chobani, which says it uses only high-quality, natural ingredients, has grown rapidly since it was founded in 2005.
Greek yogurt in general has surged in popularity as well, with fans saying they prefer its thicker consistency and relatively higher protein content when compared with the sweeter yogurt varieties that have long been sold in American supermarkets.
The private company had an estimated $244 million in revenue in 2010, according to S&P Capital IQ.
Chobani says customers with the affected code dates should contact its customer service team at email@example.com to get replacement products.