The Mexican chain pulled carnitas from menus after discovering that one of its meat suppliers was violating Chipotle's animal treatment standards.
The supplier, which Chipotle has not named, was raising pigs without access to the outdoors or to deeply bedded barns that make the animals more comfortable, the Wall Street Journal reports.
"The differences in animal welfare between pigs raised this way and pigs that are conventionally raised [are] stark, and we simply won't compromise our standards this way," Chipotle spokesman Chris Arnold told the Journal.
The violations were discovered during a routine audit, the company said. The shortage will affect one third of the chain's more than 1,700 restaurants.