Background Academic dishonesty is an intentional behavior that transgresses ethics in the teaching-learning process. The present study aimed to evaluate the factors associated with the perception of university professors about academic dishonesty in dental students from two universities in the Peruvian capital. Methods This cross-sectional, analytical study evaluated 181 professors from two Peruvian universities between March and July 2022. A validated 28-item questionnaire was used to measure the perceived academic dishonesty of their students. A logit model was used to evaluate the influence of the variables gender, marital status, place of origin, academic degree, specialization, academic area, years of teaching experience, scientific publications, ethical training and university of origin, considering a significance level of p < 0.05. Results According to the median, professors perceived that their students sometimes had attitudes and motivations to commit academic dishonesty. The professors whose origin was the capital city were twice as likely to perceive dishonest attitudes in dental students as those whose origin was a province (OR = 2.04; 95% CI: 1.06–3.93). University professors in pre-clinical courses were 0.37 times less likely to perceive dishonest attitudes than those teaching in the dental clinic (OR = 0.37; CI: 0.15–0.91). University professors in basic science courses and professors in preclinical courses were 0.43 times (OR = 0.43; CI: 0.19–0.96) and 0.39 times (OR = 0.39; CI: 0.15–0.98) less likely to perceive dishonest motivations in their students compared to university professors in the dental clinic. Gender, marital status, academic degree, specialty, years of teaching experience, scientific publications and ethical training were not found to be influential factors (p > 0.05). Conclusion Although all university professors surveyed perceived dishonest attitudes and motivations in their students, university professors from the capital city perceived such attitudes more. In addition, being a preclinical university professor was a hindered factor for perceiving such dishonest attitudes and motivations. It is advisable to implement and constantly disseminate regulations that empower academic integrity as well as to manage a system for reporting misconduct and to make students aware of the impact of dishonesty in their professional training.