Presenting himself /herself readily available at the place of employment /work on time by every employee is a basic discipline of employment irrespective of the job position held. Any compromise or lenience in this aspect of punctuality in attendance will have its cyclical effect on the day-to-day activities of an organization itself as well as its external stakeholders. Therefore, normally, no imputation of bias can be ascribed on the part of a person responsible to watch and ensure the attendance of the employees in the establishment.
However, the happening of certain contingencies beyond the control of an individual employee at times cannot be simply brushed aside by the employer. That's why provision for late attendance is made in the code of conduct or service regulations in every organization. This may be by providing of grace time of some minutes for attendance, limiting those occasions to a certain extent in a month, treating the late attendance above the limit as any leave at the credit of the late Comer and the like. The HR is expected to follow this procedure strictly and the extreme action of proportionate deduction of wages /salary cannot be right. Better, you may prefer an appeal to the chief through your functional head.