You could create a policy where if any employee is late more than 3 or 5 times in a month, taking into account a grace period of, let's say, 10 minutes, then appropriate leave will be deducted from their account.
For being 30 minutes late, half a day of leave will be deducted. For being more than 30 minutes late, a full day will be deducted. This policy applies to late arrivals that are not informed in advance.
For late arrivals that are informed, employees can be asked to compensate by staying back for the day or the following day. Deducting salary is not considered a good practice.
Thank you.