Misconduct in academic research is undoubtedly increasing, but studies estimating the prevalence of such behaviour suffer from biases inherent in researching sensitive topics. We compared the unmatched-count technique (UCT) and the crosswise-model (CM), two methods specifically designed to increase honest reporting to sensitive questions, with direct questioning (DQ) for five types of misconduct in the biological sciences. UCT performed better than CM and either outperformed or produced similar estimates to DQ depending on the question. Estimates of academic misconduct increased with decreasing seriousness of the behaviour, from c. 0% for data fabrication to >68% for inappropriate co-authorship. Results show that research into even minor issues of misconduct, is sensitive, suggesting that future studies should consider using specialised questioning techniques as they are more likely to yield accurate figures.