Budwig's theories on cancer contradicted prevailing medical views, leading to significant conflict with the mainstream medical community. Her protocol was often dismissed as unproven and potentially dangerous.

A major criticism of the Budwig Protocol was the absence of rigorous, peer-reviewed clinical trials to support its efficacy. Critics argued that anecdotal evidence was insufficient to justify its use as a cancer treatment.

Budwig faced accusations of promoting misinformation and false hope to vulnerable patients seeking cancer cures. Some medical professionals expressed concern that her protocol could lead patients to forgo conventional treatments, potentially jeopardizing their health.