Abstract Background Duplicate and salami publication are unethical, but are common practices with substantial consequences for science and society at large. Scientific journals are the ‘gatekeepers’ of the publication process. We investigated journal policies on duplicate and salami publication. Methods In 2018, we performed a content analysis of policies of journals in the disciplines of ‘epidemiology and public health’ and ‘general and internal medicine’. Journal policies were searched, extracted, coded and cross-checked. The associations of disciplinary categories and journal impact factors with journal policies were examined using Poisson regression models with a robust error variance. Results A total of 209 journals, including 122 in epidemiology and public health and 87 in general and internal medicine, were sampled and their policies investigated. Overall, 18% of journals did not have any policies on either practice, 33% only referred to a generic guideline or checklist without explicit mention about either practice, 36% included policies on duplicate publication and only 13% included policies on both duplicate and salami publication. Having explicit journal policies did not differ by journal disciplinary categories (epidemiology and public health vs general and internal medicine) or impact factors. Further analysis of journals with explicit policies found that although duplicate publication is universally discouraged, policies on salami publication are inconsistent and lack specific definitions of inappropriate divisions of papers. Conclusions Gaps exist in journal policies on duplicate and salami publication, characterized by an overall lack of explicit policies, inconsistency and confusion in definitions of bad practices, and lack of clearly defined consequences for non-compliance. Scientific publication and the academic reward systems must evolve to credit good research practice.