"People won't understand that this company is [taking] an abundance of caution," Cramer said on "Squawk on the Street." "I think they are going to spend more time in the penalty box than normal."
Chipotle closed 43 restaurants indefinitely in Washington state and Oregon amid an E.coli outbreak, adding to the company's troubles.
"Timing of reopening will be dictated by the progress and pace of the investigation. That is the top priority now," Chipotle Communications Director Chris Arnold said in a statement. He also said that no cause for the outbreak has been determined.