The companies that the F.D.A. cited have been performing liposuction to remove belly fat from patients, extracting stem cells and then injecting those cells back into the patients to treat various ailments.

On Friday, the agency said, federal marshals seized 500 doses of live Vaccinia virus vaccine for smallpox belonging to StemImmune Inc., a San Diego firm that develops stem cell-based immunotherapies for cancer. The raid came after the F.D.A. learned that the vaccine was being used to create an unapproved stem cell product, a combination of excess amounts of vaccine and stem cells derived from body fat, which was then administered to cancer patients with potentially compromised immune systems.

The F.D.A. said patients at the California Stem Cell Treatment Centers in Rancho Mirage and Beverly Hills, Calif., received the treatment made with the smallpox vaccine. It also said it had serious concerns about how StemImmune obtained the vaccine for use in an unapproved and potentially dangerous treatment.

StemImmune obtained at least some of the vaccine from the Centers for Disease Control and Prevention, according to Thomas Skinner, a C.D.C. spokesman. In its request, the company said it was conducting cancer research involving the vaccinia virus, and needed to vaccinate researchers — a seemingly legitimate reason. The company did not tell the C.D.C. that it was going to inject the vaccine into patients, he said.

A statement from StemImmune said the company had lawfully obtained the drug.

The F.D.A. also issued a warning letter to U.S. Stem Cell, a private clinic in Sunrise, Fla. The company was the subject of a March report in The New England Journal of Medicine, describing how one woman went blind and two others suffered severe, permanent eye damage after being given shots of stem cells, extracted from fat, into their eyes.