The company said that an independent lab found three samples of green onions that appeared to have a harsh strain of the bacteria.
Taco Bell said that the tests are not conclusive, but that it immediately notified health authorities and its restaurants while it awaits a final analysis.
"In an abundance of caution, we've decided to pull all green onions from our restaurants until we know conclusively whether they are the cause of the E.coli outbreak," said Greg Creed, president of Irvine, Calif.-based Taco Bell.
Taco Bell said that conclusive results will be immediately announced when available. It established a toll-free telephone number, 1-800-TACO BELL, for those with concerns about the outbreak, including customers and workers.
The chain on Tuesday reopened Long Island, N.Y., restaurants linked to the E. coli outbreak, but closed nine outlets in suburban Philadelphia after health officials reported an E. coli outbreak that sickened four people there.
Health officials have not yet been able to pinpoint the source of the bacteria that has sickened at least three dozen people in New York, New Jersey and Pennsylvania. Nine people remained hospitalized in New York and New Jersey, including an 11-year-old boy in stable condition with kidney damage.
On Tuesday, Taco Bell representatives and state and federal health inspectors visited a food distribution center in Burlington, N.J., that supplied the Long Island and New Jersey restaurants patronized by people who were sickened.
"It involves tracking your way back and trying to see if by process of elimination you can determine the root cause," said Bart McKay, a lawyer for the distributor, Texas-based McLane Co.
E. coli is found in the feces of humans and livestock. Most E. coli infections are associated with undercooked meat. The bacteria also can be found on sprouts or leafy vegetables such as spinach. The germs can be passed from person to person if they do not thoroughly wash their hands after using the bathroom.
New Jersey's health commissioner has said the most recent case of E. coli was reported Nov. 29, so the danger of infection might have passed.
Two of the New Jersey restaurants implicated were inspected and remained open. The third, in South Plainfield, remained closed Tuesday evening.
Taco Bell Corp., a subsidiary of Yum! Brands Inc., said Tuesday it had sanitized the Long Island restaurants.
Pennsylvania officials were working to determine if the outbreak there was linked to the New York and New Jersey cases. Three of those who fell ill at the end of November had eaten at a Taco Bell, state Health Department spokesman Troy Thompson said. Two were hospitalized and released.
The nine Taco Bell restaurants located in suburban Philadelphia were voluntarily closing as a precaution, the Montgomery County health department said.
In New York, Irene Abbad stopped at a Taco Bell on Long Island on Tuesday, but she was afraid to eat the food and ordered only a soft drink.
After hearing about the outbreak, she called her son, who she said is a frequent Taco Bell customer. "I said, `Don't eat Taco Bell for a while."'
E. coli, or Escherichia coli, is a common and ordinarily harmless bacteria, but certain strains can cause abdominal cramps, fever, bloody diarrhea, kidney failure, blindness, paralysis, even death.
Earlier this year, three people died and more than 200 fell ill from an E. coli outbreak that was traced to packaged spinach grown in California.