Background General practitioners (GPs) play a critical role in facilitating injured workers return to work via their ability to certify capacity to return to employment. However, little is known about the sickness certification patterns of GPs in the context of workers compensation claims. Aim To determine if GPs sickness certification behaviour has changed between 2003 and 2010 in Victoria, Australia. Method Retrospective population-based cohort study of all injured workers with an accepted compensation claim. Sickness certification rates per 1,000 working population per annum were calculated. General regression models adjusted for workers age and annual claim number were fitted to summarize changes in count and duration (expressed as incidence rate ratios or IRRs) of unfit for work (UFW) versus alternate duties (ALT) certificates within six categories of work-related injury and disease. Results 92,134 UFW and 28,293 ALT certificates were identified. A significant decrease in the unadjusted annual certification rates per 1,000 working population was observed. However, after adjusting for the annual number of claims and age, the IRRs of certificates increased over time. The rate of injuries and IRRs of certificates varied across affliction categories, IRRs being higher in mental health conditions in women than in men (IRR: 0.40, 95 CI 0.38-0.41 vs. IRR: 0.17, 95 CI 0.16-0.18). The duration of certificates remained stable, with the ALT being longer than UFW certificates in all claimants. Conclusion Our findings indicate that GPs in Victoria issue an increasing number of UFW sickness certificates each year. Further research is required to investigate the reasons for such practises.