In 1993, while Clark lived and practiced in Indiana, a former patient complained to the Indiana attorney general. An investigator for the Indiana Department of Health and a deputy attorney general visited her office incognito as part of a sting operation. Clark proceeded to test the investigator and "told him he had the HIV virus [sic], but said that he did not have cancer." She told the investigator that she could cure his HIV in 3 minutes, but that he would "get it back" unless he committed to returning for six more appointments. She then ordered blood tests from a laboratory. Upon learning of the undercover investigators' status, Clark stated that everything she had told them had been a "mistake".
In September 1999, Clark was found and arrested in San Diego, California, based on a fugitive warrant from Indiana. She was returned to Indiana to stand trial, where she was charged with practicing medicine without a license. The charge was later dismissed for failure of speedy trial. The judge's verdict did not address the merits of the charges but only the issue of whether the delay had compromised Clark's ability to mount a defense and her right to a speedy trial.
In February 2001, Mexican authorities inspected Clark's Century Nutrition clinic and ordered it shut down, as the clinic had never registered and was operating without a license. In June 2001, the Mexican authorities announced that the clinic would be permitted to reopen, but was prohibited from offering "alternative" treatments. The clinic was also fined 160,000 pesos (about $18,000), and Clark was barred from working in Mexico, even as a consultant; however, the San Diego Union-Tribune reported in 2003 that there was evidence that Clark continued to work at the clinic.
Hulda Clark has been criticized because her claims lack scientific validity and consist of anecdotal evidence. Joseph Pizzorno, a prominent naturopathic physician, evaluated Clark's claims and found that her books mixed patients with conventionally diagnosed cancer with those whose cancer diagnosis was based solely on her use of the "Syncrometer". The patients with medically diagnosed cancer did not respond to Clark's treatment, while those she had diagnosed using the "Syncrometer" were "cured". Pizzorno concluded that Clark's treatments were ineffective and that treatments based on Clark's recommendations "pose a substantive public health danger".
The Swiss Study Group for Complementary and Alternative Methods in Cancer (SCAC) issued a strong warning to cancer patients considering Clark's methods:
There is no scientific basis for Hulda Clark's hypotheses and recommendations, including her suggested treatments. The parasite Fasciolopsis buskii does in fact exist, but only in Asian countries, so that an infection in our country is ruled out. Consequently, this parasite does not enter into consideration as a cause of the numerous cases of cancer in the Western countries; at most, it might be one of several causes of liver cancer (and only for this type of cancer) in the Asian countries. As a whole, Clark's thesis cannot be comprehended, nor is it proven. In individual cases, her advice can be very extensive and costly. Hence if patients do not apply her method consistently and their disease continues to progress, they run the risk of attempting to blame themselves for this, rather than Clark's treatment which is ineffective, as viewed at present.
Prominent alternative medicine proponent Andrew Weil has written, "No studies have backed up [Clark's] bizarre claims, and it’s unclear whether the cancer patients she’s supposedly cured ever had cancer to begin with."
In 2002, the San Diego Union-Tribune reported that Clark and her son Geoff operated a restaurant and leased housing for patients at Clark's Tijuana clinic. The article described a couple whose daughter, suffering from spinal muscular atrophy, was treated for 10 months by Clark at a cost of approximately $30,000 without improvement. Despite the cost and lack of improvement, the couple stated that Clark insisted she was close to curing the child, and that stopping treatment might endanger her. The patient's mother stated: People don’t understand why we stayed so long, but Hulda Clark did a very good job of preying on us.While stating she could not respond to the parents' allegations on grounds of patient confidentiality, Clark denied their statements in general.