The company had closed the restaurants on Oct. 31 after health officials linked 11 Chipotle outlets to some cases of food poisoning caused by the bacteria.

Health officials concluded that there is no ongoing risk from the incident, Chipotle said on Tuesday.

The burrito chain said it would replace all ingredients at the restaurants and reopen them in the "coming days".

Shares of the company, known for using organic ingredients and antibiotic-free meat, were up 2.4 percent at $623.96 in morning trading.

The Oregon Health Authority had said on Nov. 1 that three cases of E. coli in Oregon and at least 19 in Washington had been linked to eating at Chipotle restaurants since Oct. 14.

One third of the affected customers had been hospitalized, but no deaths were reported, the health authority had said.

On Monday, health officials said food samples taken from the restaurants found no presence of E. coli bacteria.

Food outbreak investigations do not always identify a specific food source as the culprit, because contaminated food is at times consumed before the samples are collected, the Washington health department has said.

Chipotle had earlier seen two separate outbreaks of salmonella and the highly infectious norovirus due to food contamination.

Up to Monday's close, Chipotle's shares had fallen nearly 5 percent since the company announced the closure of restaurants.