"It's a really tough time, I'm sorry for the people who got sick," Ells said on "The Today Show." "They're having a tough time. I feel terrible about that. We're doing a lot to rectify this."
Ells said new testing and food safety practices are currently being implemented that will put the chain "10 to 15 years ahead of industry norms."
"I believe it will be the safest restaurant to eat at," Ells said.
A spokesman from Chipotle said that the recently-closed restaurant in the South Lake Union neighborhood of Seattle was under investigation.
"We have one restaurant in Seattle that is closed because of an issue around hot holding temperatures. We are looking into a cause of that and will address it," a spokesman said in an email.
The Seattle Health Department said in a blog post that all Seattle-based Chipotle restaurants have been under close watch after they reopened following the E.coli outbreak. The health department said there had been red violations on three separate days at the location that was closed and that meat was held at temperatures that were too low.
"Red violations indicate improper practices or procedures identified as the most prevalent in contributing to food-borne illness," the department said.
Chipotle has already been battling two recent health-related outbreaks. The cause of the E.coli outbreak that sickened at least 52 people has not been found. Ells said on "Today" that the company has performed "thousands and thousands of tests" on ingredients and surfaces looking for signs of the bacteria.
Chipotle has announced it's taking multiple steps to improve food safety.
"Work on our enhanced food safety program began immediately after reports surfaced at the end of October regarding the E.coli cases in Washington and Oregon," the company said in a statement. "The enhanced food safety program is the product of a comprehensive reassessment of our food safety practices conducted with IEH Laboratories that included a farm-to-fork assessment of each ingredient we use with an eye toward establishing the highest standards for safety."
The new measures to ensure food safety and handling include testing fresh produce with DNA-based tests, starting end-of-shelf-life testing to ensure ingredients are safe throughout their shelf life, measuring performance data of vendors and suppliers and enhancing employee training in food safety and handling, according to the company.