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Background Research misconduct is a global concern in almost every scientific field. There is no comprehensive data regarding the prevalence of research misconduct among Iran's medical faculties. This study aims to conduct a nationwide survey regarding research misconduct in the faculty members of medical universities in Iran. Methods We used the Persian version of the research misconduct questionnaire (PRMQ) in an online survey on the Google Forms platform. Using Google Froms, the survey link was sent to a systematic random sample of medical faculty members in Iran (N = 4986). Descriptive analyses were performed on the individual items of PRMQ, with frequencies and percentages for categorical and Likert-type response items and means and standard deviation (S.D.) for continuous variables. Chi-square analysis was conducted to test hypotheses examining differences in frequency of responses related to factors influencing misconduct. All the analyses were performed using R 3.6.0. Results The response rate was 13.8% (692 responses). Nearly three-quarters (N = 499, 72.1%) of the respondents had first-hand witted some instances of research misconduct during the previous year. Academic scholars in various tenure categories rated investigator competitiveness differently (df:9, p = 0.008), with the highest difference in the mean scores between tenure categories one (TC1) (2.7, SD:0.87) and four (2.4, SD:0.77). Only 18.5% of participants perceived the effectiveness of their associated organization’s rules for reducing research misconduct to be high or very high. Pressure for tenure was identified as the most perceived as having a strong behavioral influence on engaging in research misconduct (80.2%). Conclusions Research misconduct is a living trouble among medical faculty members in Iran and needs a more proactive approach to tackle.