The Food and Drug Administration halted the sale of four types of R. J. Reynolds cigarettes on Tuesday, saying the company failed to prove that they were not more harmful than products already on the market.

The agency ordered retailers who sell any of the cigarettes to stop immediately and to dispose of them within 30 days or face financial penalties or criminal prosecution.

Under a 2009 federal law, the F.D.A. can reject cigarettes and other tobacco products that its scientists believe pose greater public health risks than comparable products on the market, a sharp departure from previous practice, when tobacco companies could change existing products and introduce new ones at will.

The four cigarettes the agency ordered removed on Tuesday — Camel Crush Bold, Pall Mall Deep Set Recessed Filter, Pall Mall Deep Set Recessed Filter Menthol and Vantage Tech 13 — were introduced during a grace period set up by the law that ended in 2011. R. J. Reynolds applied for so-called substantial equivalence status at that time. To be considered substantially equivalent, tobacco products must be shown to have the same characteristics as a product already on the market or, if different, raise no new questions for public health.

The agency has considered hundreds of applications since the law was passed, and has allowed the brands to proceed at about double the rate that it has blocked them, F.D.A. officials said.

“These decisions were based on a rigorous, science-based review designed to protect the public from the harms caused by tobacco use,” Mitch Zeller, the director of the Center for Tobacco Products at the agency, said in statement.

The agency ruled the four R. J. Reynolds products were not the same as their predecessor brands. That left open the possibility that they were more harmful.

In a statement, R. J. Reynolds said it “strongly disagrees” with the decision. Jeffery S. Gentry, the company’s executive vice president for operations and chief scientific officer, said in the statement, “Our submissions to the agency on these brands were comprehensive, and we believe we effectively demonstrated substantial equivalence.”

He did not say what further actions the company would take, only that it was “examining all of our options.”

The F.D.A.’s scientists considered ingredients, engineering and chemistry and studied how they might influence the cigarettes’ toxicity, addictiveness and appeal to smokers. Camel Crush Bold cigarettes, for example, included a small menthol capsule in the filter that raised questions about whether it could make the cigarette more appealing for consumers.

Matthew Myers, the president of Campaign for Tobacco-Free Kids, said the products “deliver menthol differently and at higher levels, have added sugars and other sweeteners, new filters, and tested differently for harmful and potentially harmful constituents.”

Cowen and Company, a financial services firm, said in a research note that the four banned products made up less than 1 percent of R. J. Reynolds’s cigarette sales volume, so the action is not likely to be a major financial issue for the company.

It said R. J. Reynolds would probably file a legal injunction to have the action suspended, or pull the products and then contest the findings legally.