Abstract Background Regarding the objective of preventing early exits from labor market, the late life-course years present an important timeframe. It is essential to identify the employees in the greatest risk of permanently losing their work ability. In practical applications, multifactorial models are needed to evaluate the combined effect of risk factors. In this study, the disability pension risk is modeled based on large unique register data, at the same time assessing the effect of sickness absences (SA) of different lengths. Methods We utilize a logistic model for the risk of filing a first-time disability pension application (DPA) based on register data on 222,321 Finnish municipal sector employees. The data include employment and sickness spells, occupations, and wages in 2016-2018 as covariates. During the 3-year follow-up, 2,969 employees filed a DPA. The data include also short SA spells, a novelty in these kinds of studies. DPA is used as a follow-up to include employees who receive a rejecting decision but still carry a physician’s evaluation of diminished work ability. Results The resulting model can accurately predict the risk of DPA in employee groups. Age, occupation, cumulative SAs preceding the application, and the number of SA spells of all lengths, also short ones, have a significant increasing effect on the DPA risk. Proximity of the retirement age and high earnings decrease the risk of DPA. Surprisingly gender had no effect on the risk. Conclusions The results indicate that register-based sociodemographic data is very useful in modeling the employee DPA risk in public sector employee groups. The resulting model provides a basis for tools for predicting the risk status of employee groups for the use of employers responsible for risk management and early intervention, also allowing for the assessment of economic effects of SAs and disability risk. The presented modeling results are already utilized among public sector employers in Finland. Key messages • Disability pension risk can accurately be predicted in public sector employee groups based on readily available sociodemographic register data. • All sickness absences have a significant increasing effect on the risk of disability pension application, but the effect varies greatly depending on age and occupation.