FDA Commissioner Scott Gottlieb, in a statement on the case, said the agency “will not allow deceitful actors to take advantage of vulnerable patients by purporting to have treatments or cures for serious diseases without any proof that they actually work.”

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For years, critics of stem-cell clinics performing unproven treatments have called on the FDA to take action against them. One of them, Paul Knoepfler, a biologist at the University of California at Davis, said Monday that the new enforcement actions, coupled with a separate Gottlieb statement on the future of stem-cell therapies, “looks like positive news." He added, “I feel encouraged that this is a big step in the right direction."

StemImmune responded that it has “fully cooperated with the FDA about the development of its stem-cell based cancer therapy" and that no patients have suffered ill effects from the treatment. Mark Berman, a Beverly Hills plastic surgeon who was a co-founder of California Stem Cell Treatment Centers, called Gottlieb's comments “libelous," and added, “We're not ignoring the FDA and we aren't renegade doctors."

In a separate enforcement action, the agency on Monday posted a warning letter issued last week to U.S. Stem Cell of Sunrise, Fla., saying that recent FDA inspections of the clinic found that it was processing body fat into what's called stromal vascular fraction — stem cells derived from body fat — and administering the product both intravenously and directly into the spinal cord of patients to supposedly treat a variety of serious diseases or conditions, including Parkinson’s disease, ALS, and heart and lung disease.

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The FDA said it has not approved any products manufactured by U.S. Stem Cell and that it had documented “significant deviations" from current good manufacturing practices in at least 256 lots of stem cell products. The agency also said the clinic tried to impede the FDA’s investigation by refusing to allow entry except by appointment and by denying FDA investigators access to employees.

The clinic in March was the subject of a New England Journal of Medicine article that said three women with age-related macular degeneration were blinded or had their vision badly damaged after stem cells were injected into their eyeballs.

In a statement, U.S. Stem Cell said that “the safety and health of our patients are our number one priority and the strict standards that we have in place follow the laws" of the FDA. It said that it has never had a “breach of sterility and our facility has demonstrated sterile surgical techniques as required by the state medical boards."

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Stem-cell clinics offering unapproved — and unproven — treatments have sprung up by the hundreds across the country over the past several years. Many offer fat-derived injections that supposedly treat everything from hip and knee problems to autism and Alzheimer's disease.

In many cases, the therapies involve liposuction — extracting stem cells from patients and processing them with enzymes and other materials — and then re-injecting them at different places in the body. Despite the proliferation of clinics, most stem-cell research remains at an early stage, and the FDA has approved only a few therapies, for blood disorders.

Gottlieb, in the statement about the regulation of stem-cell therapies, said that the emerging field of cell-based and so-called regenerative medicine holds “significant promise for transformative and potentially curative treatments” for serious illnesses but that “a small number of unscrupulous actors” is putting the field at risk. He said he is launching a new working group at the FDA “to pursue unscrupulous clinics through whatever legally enforceable means are necessary to protect the public health."

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At the same time, he said, the agency will develop a framework to more clearly describe the “rules of the road” for the field and to allow responsible developers of stem-cell treatments to more easily win FDA approval. “The FDA must advance an efficient and least burdensome framework as a way to help new products remain compliant with the law through a regulatory structure that does not become a barrier to beneficial new innovation,” he said.

He said, for example, that FDA might not require advance approval for treatments where cells or tissues are extracted and given back to the same individual or when the materials do not undergo significant manufacturing and are intended to perform the same basic functions as they did originally. But when the significant manufacturing occurs or the cells or tissues are targeted for a different purpose, greater uncertainty exists and pre-market review is required, he said.

In the California case, the FDA said it had “serious concerns” about how StemImmune obtained the smallpox vaccine, which is not commercially available. The vaccine typically is reserved for people at high risk for smallpox, such as members of the military.

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The vaccine is made from a live virus called vaccinia, which is a poxvirus that is similar to smallpox but less harmful. The vaccine can't cause smallpox, but for people with compromised immune systems — as is the case with many cancer patients — exposure can result in life-threatening medical problems, including myocarditis, which is an inflammation of the heart muscle.

StemImmune obtained at least some of the vaccine from the Centers for Disease Control and Prevention, which controls the civilian supply. Thomas Skinner, a CDC spokesman said that the company had requested the vaccine to inoculate researchers who were doing cancer research involving the vaccinia virus.

In recent years, the vaccine, which was used to stamp out smallpox, has increasingly been tested as an anti-cancer tool, including as a way to prompt the immune system to attack malignancies.

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Leigh Turner, a bioethicist at the University of Minnesota, welcomed the FDA's moves, but disputed Gottlieb's assessment that there was just a "small number" of unscrupulous players. He said there are hundreds of clinics offering unapproved treatments for a slew of diseases and that patients are being injured. "The question is," he said, "will the FDA take action on hundreds of these clinics?"