Rationale, aims and objectives Financial conflicts of interest (FCOI) between pharmaceutical companies (Pharma) and healthcare domains may unduly influence physician-led clinical practice and patient-centered care. However, the extent of awareness and perceptions of FCOI among Japanese cancer patients remains unclear. This study aimed to assess these factors and their impacts on physician trustworthiness among Japanese cancer patients. Methods A cross-sectional study using self-administered surveys was conducted on a Japanese cancer patient advocacy group with 800 registered members from January to February 2019. Main outcome measures included awareness and perceptions of physician-Pharma interactions, their impact on physician trustworthiness, and attitudes towards FCOI among professions. We also performed thematic analyses on additional comments responders provided in the surveys. Results Among the 524 invited members, 96 (18.3%) completed the questionnaire. Of these, 69 (77.5%) were cancer patients. The proportion of participants aware of such interactions ranged from 2.1% to 65.3%, depending on the interaction type. Participants were generally neutral on how the interactions would affect physician trustworthiness. A large proportion of participants agreed that these interactions were unethical, could influence physicians’ prescribing behavior leading to unnecessary prescriptions, and negatively affect physician trustworthiness. Qualitative responses (n=56) indicated that patients expected physicians to use sound ethical judgment and avoid accepting incentives. Participants were also concerned about their treatment and the undue influence of FCOI on physicians. Conclusion Most participants were aware of at least one FCOI between Pharma and physicians and perceived them negatively. Further efforts to regulate FCOI appear necessary to protect patient-centered care.