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Purpose–This paper seeks to discover the factors that influence the supervisor to give the punishment level to civil servant staff—the data being used is a questionnaire to several civil servants in public academic institutions.

Methodology/approach–This research used computational tools to classify transgressions into punishment categories (light, medium, or severe) with the model using the data science technique based on the partial least square-structural equation modeling (PLS-SEM) approach.

Findings–It was found that the model of civil servant discipline in Indonesia is based on 14 hypotheses from bootstrapping technique and by using data science technique to support the result analysis of PLS-SEM.