Elite military trainees are burdened by high numbers of musculoskeletal (MSK) injuries and are a priority military population for injury prevention. This research aims to describe the MSK complaint epidemiology of trainees undertaking special forces (SF) training in the Australian Defence Force (ADF). One barrier to accurate injury surveillance in military populations is that traditional surveillance methods rely on personnel engaging with the military healthcare system to collect injury data. This approach is likely to underestimate the injury burden as it is known that many military personnel, particularly trainees, avoid reporting their injuries because of various motives. Subsequently, the insights from surveillance systems may underestimate the injury burden and limit the ability to inform prevention requirements. This research aims to actively seek MSK complaint information directly from trainees in a sensitive manner to mediate injury-reporting behaviors. This descriptive epidemiology study included two consecutive cohorts of ADF SF trainees from 2019 to 2021. Musculoskeletal data items and their respective recording methods were based on international sports injury surveillance guidelines and adapted to a military context. Our case definition encompassed all injuries or physical discomforts as recordable cases. A unit-embedded physiotherapist retrospectively collected MSK complaint data from selection courses and collected prospective data over the training continuum. Data collection processes were external to the military health care system to mediate reporting avoidance and encourage injury reporting. Injury proportions, complaint incidence rates, and incidence rate ratios were calculated and compared between training courses and cohorts. In total, 334 MSK complaints were reported by 103 trainees (90.4%), with a complaint incidence rate of 58.9 per 1,000 training weeks (95% CI, 53.0-65.5). Of these MSK complaints, 6.4% (n = 22) resulted in time loss from work. The lumbar spine (20.6%, n = 71) and the knee (18.9%, n = 65) were the most frequently affected body parts. Most of the MSK complaints were reported during selection courses (41.9%), followed by field survival and team tactics (23.0%) and urban operations courses (21.9%). Physical training accounted for 16.5% of complaints. Fast-roping training was associated with more severe MSK complaints. Musculoskeletal complaints are highly prevalent in ADF SF trainees. Complaints are more frequently reported in selection and qualification training courses than in physical training. These activities are priorities for focused research to understand injury circumstances in ADF elite training programs to inform injury prevention strategies. A strength of our study is the data collection methods which have provided greater MSK complaint information than past research; however, much work remains in conducting consistent and accurate surveillance. Another strength is the use of an embedded physiotherapist to overcome injury-reporting avoidance. Embedded health professionals are recommended as continued practice for ongoing surveillance and early intervention.