Objective To examine if the factors associated with days of absence following a work-related injury are similar for mental health versus musculoskeletal (MSK) conditions. Methods A secondary analysis of wage replacement workers compensation claims in the state of Victoria, Australia. We examined the relationship between individual, injury, occupational and workplace variables with days of wage replacement over the 2-year period following first day of absence from work separately for mental health claims and MSK claims using negative binomial regression models. Results Mental health conditions were associated with a greater number of days of absence over the 2 years following first incapacity compared to MSK conditions. Differences were observed in employment, injury and industry variables on absence from work for mental claims compared to MSK claims. Working in the agriculture, forestry, fishing and mining industries and employment with a small organisation were more strongly associated with the number of days of wage-replacement among MSK compared to mental health claims, and working in the public administration and safety, or education and training industries or being employed in a position with high time pressure were associated with greater days of wage-replacement among mental health compared to MSK claims. Conclusions Predictors of days away from work in the 2 years following an injury differ for mental health versus MSK claims. Given the increasing number of mental health claims in Australia more research is required to understand differences in return-to-work for this group of claimants compared to those with physical injuries.