The current study aimed to compare self-reported injecting and sexual risk behaviour among Needle and Syringe Program (NSP) attendees who self-completed a questionnaire to that of those who received assistance in completing the questionnaire. Information on demographic, injecting and sexual risk behaviour was collected via a self-completed questionnaire for an annual cross-sectional survey of injecting drug users (IDUs) recruited from sentinel NSPs around Australia. Assistance was provided when necessary and recorded. Of 2,035 participants, 1,452 (71%) reported completing the questionnaire without assistance. Being male and nominating a language other than English spoken at home was independently associated with receiving assistance with questionnaire completion. Participants who reported heroin as the drug last injected were also more likely to receive assistance. Multivariate analyses revealed those who received assistance with questionnaire completion were less likely to report re-using a syringe after someone else and less likely to report sex work in the past month. The current findings suggest self-completion of risk behaviour questionnaires should be considered as an alternative to interviewer administered questionnaires to maximise accuracy of self-reports.