Prevalence of research misconduct, questionable research practices (QRPs) and their associations with a range of explanatory factors has not been studied sufficiently among academic researchers. The National Survey on Research Integrity targeted all disciplinary fields and academic ranks in the Netherlands. It included questions about engagement in fabrication, falsification and 11 QRPs over the previous three years, and 12 explanatory factor scales. We ensured strict identity protection and used the randomized response method for questions on research misconduct. 6,813 respondents completed the survey. Prevalence of fabrication was 4.3% (95% CI: 2.9, 5.7) and of falsification 4.2% (95% CI: 2.8, 5.6). Prevalence of QRPs ranged from 0.6% (95% CI: 0.5, 0.9) to 17.5% (95% CI: 16.4, 18.7) with 51.3% (95% CI: 50.1, 52.5) of respondents engaging frequently in at least one QRP. Being a PhD candidate or junior researcher increased the odds of frequently engaging in at least one QRP, as did being male. Scientific norm subscription (odds ratio (OR) 0.79; 95% CI: 0.63, 1.00) and perceived likelihood of detection by reviewers (OR 0.62, 95% CI: 0.44, 0.88) were associated with engaging in less research misconduct. Publication pressure was associated with more often engaging in one or more QRPs frequently (OR 1.22, 95% CI: 1.14, 1.30). We found higher prevalence of misconduct than earlier surveys. Our results suggest that greater emphasis on scientific norm subscription, strengthening reviewers in their role as gatekeepers of research quality and curbing the “publish or perish” incentive system promotes research integrity.