Federal food safety officials said on Monday that they would ban the sale of ground beef containing six toxic strains of E. coli bacteria that have increasingly been showing up in the food supply, taking a long-delayed step that was opposed by many in the meat industry.

“This is one of the biggest steps forward in the protection of the beef supply in some time,” said Dr. Elisabeth Hagen, the head of food safety for the Department of Agriculture, which regulates meat. “We’re doing this to prevent illness and to save lives.”

The new rule means that six lesser-known forms of E. coli will be treated the same as their much more famous cousin, a strain of the bacteria called E. coli O157:H7, which has caused thousands of illnesses and prompted the recall of millions of pounds of ground beef and other products.

That strain was banned from ground beef in 1994 after it caused a major outbreak of illness that sickened hundreds and killed four children. Until now, that one strain of E. coli was the only type of dangerous bacteria to be banned from any type of fresh meat. It is not illegal to sell meat containing other types of bacteria, like salmonella, in part because cooking typically kills the pathogens. Regulators have treated ground beef differently from other meats and poultry because Americans like to eat it rare and resulting illnesses can be deadly and children are often the victims.

In recent years, however, scientists found that several other strains of E. coli in food were making people sick and they identified the six most potent, which were called the non-O57s or the Big Six.

The American Meat Institute, an industry group, was highly critical of the new policy. “Imposing this new regulatory program on ground beef will cost tens of millions of federal and industry dollars — costs that likely will be borne by taxpayers and consumers,” the group said in a statement. “It is neither likely to yield a significant public health benefit nor is it good public policy.”

Citing arguments it has made previously in opposing such a step, the group said that other measures the industry is already taking to improve food safety are sufficient to help combat the additional strains of E. coli. 

While several outbreaks caused by the Big Six E. coli strains have been linked to produce, the group pointed to the fact that only one has been tied to ground beef. In that outbreak, which occurred last year, three people were sickened.

“There is no public health crisis related to those strains in ground beef,” the group said.  The agency will begin enforcing the new rule in March, to give the meat industry time to prepare for the change. The rule will apply to hamburger meat and trim or beef scraps that go into it, as well as some other products, like steaks that have been tenderized with machines that use needles to poke minute holes in the surface. The agency will start testing meat at packing plants in March.

Some meat processors have begun to test for the six strains in recent months in anticipation of federal action, but many others will most likely begin testing once the new rule takes effect.

Under the rule, any meat that is found to contain the Big Six E. coli, in tests by government or industry, will have to be diverted for use in cooked products. The bacteria is killed by heating the meat to 160 degrees.

While the new rule significantly expands the agriculture department’s ban, it does not include all forms of toxic E. coli. A highly virulent strain of the bacteria that caused thousand of illnesses and dozens of deaths among people who ate contaminated sprouts in Europe this summer is not one of the Big Six because it has not been detected as a cause of illness in the United States.

Dr. Hagen said the list of banned pathogens might continue to grow. “This is where we started and it doesn’t rule out the possibility that we would consider other pathogens in the future,” she said. Toxic forms of E. coli produce a poison called shiga toxin. It can cause bloody diarrhea and severe stomach cramps. The most severe cases can lead to kidney failure and death.

The Agriculture Department has been weighing an expansion of its E. coli ban for at least four years. A draft of the new rule was completed in January, but it was further delayed for months in a review by the Obama administration.

The meat industry argues that an expanded ban would lead to increased costs, including for testing and holding back meat from the fresh ground beef market.

The U.S.D.A. estimated that the new rule would cost the industry up to $10 million a year for testing and diverting meat to cooked products.

Dr. Hagen also said that the rule did not conflict with the Obama administration’s push to cut back on regulation that could increase costs for business at a time of economic hardship.

“There’s really no inconsistency between having a strong economy and having a safe food supply,” Dr. Hagen said. “The administration is committed to regulate only to the extent that is necessary to protect our people.” The U.S.D.A. first moved to ban the O157 form of E. coli in 1994, after an outbreak the previous year was linked to hamburgers sold at the Jack in the Box fast food chain.

At that time, the meat industry sued to block the ban, but the agency prevailed in court.

Several advocates wondered whether the industry would now take a similar step, or whether it would ask allies in Congress to seek to bar the Agriculture Department from carrying out or enforcing its new rule.

William Marler, a Seattle lawyer who represents food poisoning victims, said he hoped the industry would not fight the expanded rule. “I would certainly urge them not to do it,” said Mr. Marler. “They lost on 0157 and I think it sends the wrong message to consumers and trading partners.”

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