Mr. Dhingra,
For your kind information 3% wages comes to one day wage. Already one day will be reduced in his attendance for his unapproved/uninformed leave (His working day will be 29, instead of 30). It will be discretion of the management to decide about fine (one day salary or fixed amount less than one day salary).
Do you think HR can decide about fine? Each & every decision will be decided by the management. Without those, HR has to answer the Finance department. It will be problem during Audit.
As you are mentioning, HR will not only concentrate on imposing fine, as they are also responsible for attrition which is their main performance criteria. Please keep in mind, imposing fine doesn't count on the performance of an HR. He/she will not get salary increment/promotion only because they are imposing fine to employees. Imposing fine will lead them to answerable to Employee, Department Manager, finance dept, statutory dept and management.
How many HR do you know, who impose fine only because of the instruction from Management and they worry for the employees??