In August, United States marshals, acting on behalf of the F.D.A., seized vials of smallpox vaccine that was being used to create a stem cell product that was being given to cancer patients at the California clinics. The product posed a risk to those patients of inflammation of the heart and surrounding tissues, the agency said.

The California center trains other physicians in how to extract stem cells and has affiliates around the country. A Florida woman, Doris Tyler, lost her sight after being treated at an affiliate, the Ageless Wellness Center in Peachtree City, Ga. Cells from her fat were injected into both eyes.

Dr. Berman said that many people had been helped by his clinic and that he had tried to work out a compromise with the F.D.A. but was unable to do so. He also said he believed the cells that are harvested from individuals do not constitute a drug and should not be regulated as such.

In its statement, the F.D.A. also said that both the U.S. Stem Cell Clinic and the California Stem Cell Treatment Center were using cell extracts to treat serious conditions — including Parkinson’s disease, amyotrophic lateral sclerosis and chronic obstructive pulmonary disease — but that their products were not approved for any use.

The F.D.A. oversight of stem cell therapies and regenerative medicine is still in flux. In August, Dr. Scott Gottlieb, the agency’s commissioner, called the field one of the most promising areas of science and medicine, holding great promise for some of the world’s most intractable illnesses. He vowed that the F.D.A. would ease the path to approval for researchers and companies that were developing legitimate treatments — a program authorized by Congress in the 21st Century Cures Act.

At the same time, however, Dr. Gottlieb vowed to crack down on clinics making hollow claims and marketing unsafe treatments. He also announced the action against the California Stem Cell Treatment Centers in Rancho Mirage and Beverly Hills and against the U.S. Stem Cell Clinic.

In November, the F.D.A. continued work along both themes.

The agency acknowledged the difficulty in pursuing rogue clinics and suggested that consumers check up on stem cell clinics before receiving treatment.