For the day of absence, if you are deducting that day's salary, it is a deduction for the absence of work, and there is no amount 'gained' by the employer. It will reflect in the paysheet as such. It will be on this amount that you will pay ESI, PF, etc.
Fines for Late Coming
However, imposing a fine for late coming is different. Though it is reflected in the paysheet as a recovery from the employee, his salary for the day will remain the same. Such amounts, i.e., fines imposed, should be utilized for labor welfare activities of the company. If you do not have any such welfare fund, you can deposit it with the Labor Welfare Fund of the government.