With increasing burden on schools and requirements for active parental consent, low student survey participation rates are problematic, including where ethnic minority students are often underrepresented in behavioural risk surveys. To improve parent permission rates and survey participation, incentive use (individual vs. group) and mode of survey administration (web-based vs. paper-pencil) were examined in a sample of ethnically diverse students (n == 2488) in the 6th, 8th, 10th and 12th grades from eight schools in Hawai`i. Mode of survey administration was also compared for student reporting of alcohol and other substance use and associated risk and protective factors. Classes were assigned to one of four conditions based on incentive type and route of survey administration. The group incentive was associated with a significantly higher rate of parental permission compared to individual incentive; however, it did not impact survey completion rate. Students who took the web-based version compared to the paper-pencil version of the survey were more likely to report use of alcohol, tobacco and other drugs in the past 12 months. The use of web-based surveys may increase reporting of sensitive behaviours such as substance use among adolescents compared to paper-pencil versions