It is not a deduction. Deductions are amounts like taxes taken out of pay that are owed to an outside entity. What you describe is a reduction of earnings. So, if someone normally earns 1000 for 40 hours of work, but is late and misses one hour, pay them 975 for 39 hours.
If you want to show this explicitly on a payslip, you can enter a negative quantity on a separate earnings line.