The Denver-based chain said in a statement that consumers want to know whether the food they're eating has been genetically modified.
"But well-funded opposition groups continue to fight labeling efforts, with opponents putting their own profits ahead of consumer preferences," Chipotle CEO Steve Ells said.
The company has not donated to the Colorado or Oregon labeling campaigns.
The two states' proposals would require manufacturers, retailers and suppliers to label raw and packaged foods produced entirely or partially by genetic engineering. The measures wouldn't apply to food served in restaurants, though Ells said Chipotle voluntarily labels GMO foods online.
The federal government does not require labeling of genetically engineered foods.
Three states — Vermont, Maine and Connecticut — have passed labeling laws, although they don't take effect immediately. Similar labeling measures in California and in Washington state failed narrowly in recent years after millions of dollars were spent, mostly by labeling opponents.
Opponents of the labeling requirements say mandatory labels would mislead consumers into thinking engineered ingredients are unsafe, which scientists have not proven. They include food corporations and biotech companies that grow engineered crops.
If approved, the Colorado and Oregon requirements would take effect in January 2016. Colorado started mailing ballots to voters Tuesday, while Oregon will begin Wednesday.
In Colorado, opponents of the GMO labeling requirements have vastly outspent proponents. They have raised about $9.7 million, compared with about $334,000 for supporters, according to Colorado campaign finance disclosures.
Colorado's labeling campaign came from a citizen petition. The state Legislature has considered but rejected mandatory GMO labeling.
A spokeswoman with Colorado's No On 105 Coalition said Tuesday the costs of complying with the proposed labeling requirements — including ingredient substitution and product segregation — would end up increasing the price of food.
"Restaurants are exempt from Proposition 105's requirements, so Chipotle apparently supports voluntary labeling standards for themselves and mandatory labeling for others," Sara Froelich said in a statement.
A spokesman for the measure's proponents, Right To Know Colorado, called Chipotle's endorsement "very big" for the effort.
"They're an important company in Colorado, and they're standing up and saying, 'You're right. Consumers should know what's in their food,'" Larry Cooper said.
In Oregon, opponents of the labeling measure have raised $7.3 million, while proponents have raised $4.8 million.
Associated Press writer Gosia Wozniacka in Portland, Oregon, contributed to this report.
Kristen Wyatt can be reached at http://www.twitter.com/APkristenwyatt