The company said the vast majority of its stores in the area had reported no problems. "We offer our deepest sympathies to those that have been affected by this situation."
It is the third outbreak of food contamination at Chipotle restaurants since August. Those earlier cases involved salmonella and the highly infectious virus norovirus.
"Short term they (Chipotle) will take a hit but it will blow over quickly. They have a lot of customer goodwill." said Bob Goldin, executive vice president at U.S. restaurant consulting firm Technomic.
The 1,700-outlet chain has grown quickly since it opened in 1993 with a single location, distinguishing itself from typical fast-food restaurants by touting its use of healthy and high-quality fresh ingredients in its menu of burritos, tacos and salads.
There is a growing trend among restaurants, as with Chipotle, to use more fresh, unprocessed food. While that may be good for nutrition, experts say it raises the risk of foodborne illness because cooking kills pathogens that cause illness.
The Oregon Health Authority said three cases of E. coli in Oregon and at least 19 in Washington have been linked to eating at Chipotle restaurants since Oct. 14, with ages ranging from 11 to 64. One third of affected customers have been hospitalized, but no deaths have been reported.
But more cases are likely to be reported, the agency said, because some people who may have been infected with the intestinal bug likely have not yet sought medical care.
"Health officials want people who have eaten at a Chipotle between October 14 and 23, and become ill with vomiting and bloody diarrhea, to see their health care provider and mention this outbreak," the agency said in a notice on its website.
E. coli is among a vast array of bacteria that live in the human gut and which cause no problems. But some strains can cause serious symptoms and even be life-threatening, and are spread by oral contact with fecal matter.
The incidents come on the heels of contamination outbreaks from other pathogens at the chain's restaurants in Minnesota and California this summer.
Minnesota health officials in September said tomatoes used in 22 of Chipotle's restaurants infected dozens of patrons the month before with salmonella, including some who were hospitalized, largely in the Minneapolis-St. Paul area. The company has since switched tomato suppliers.
Public health officials in Simi Valley, California, in August confirmed that the contagious norovirus was the reason about 80 customers reported feeling ill after eating at a local Chipotle restaurant.
The virus, which causes symptoms similar to those caused by E. coli, can be contracted from an infected person or from contaminated food, water or surfaces.
Food poisoning outbreaks at restaurant chains happen infrequently, and often trigger lawsuits. But sales tend to recover relatively quickly, as seen in cases involving Taco Bell in 2011 and Subway in 2008, unless the contaminations are lethal.
Jack in the Box almost collapsed in 1993 after four children died from eating contaminated and undercooked meat at that chain. The outbreak caused a national panic and the company rebounded by strengthening its food safety systems and investing in a major advertising campaign.