Late Filing Of Official Business Form

Is there a rules/laws on salary deduction everytime an employee is late in filing of Official Business Form/Leave Form? Is it ok to deduct it from their salary without refund (in case they filed after?

There should be an existing internal policy pertaining to timekeeping and attendance particularly the filing of OB / Leaves. If at present you don't have any written policy on this then I dont think you can deduct from your employee. If the employee applies for OB/Leave on a later date and if that application was approved by the supervisor then that application is already authorized or accepted hence a refund is in order. You can put the supervisor liable since he/she approved the late application.
Law wise, maybe a deduction is authorized if the employee is a daily/hourly paid employee.

What if theres is an internal policy on this. It indicates that "Salary deduction with refund for late filing (not late approval) will be granted on first offense, Salary deduction without refund will be meted on the succeeding offenses. Offenses will be reset on the first day of the month". Does we violated the law (if any)?
The employee is paid on a monthly basis.

If there is an existing policy on this then I suggest that if you find any violation in your policies, try to conduct due process of sending the employee the twin notices before you implement any sanction to the employee.