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Employee Missing From a Payroll Run: the Four Things to Check

Why an employee (or every employee) is absent from a payroll run — payroll center assignment, payroll month sequence, payroll cycle inclusion, and statutory registration — and how to fix each one.

 If an employee is missing when you run payroll, check in this order:

1. Is the employee assigned to the payroll center you are running?

The employee must be assigned to the payroll center of the run. Click into the Employee Profile > Payroll tab and check the Payroll Center configuration. Ensure that the employee has been assigned to the payroll cycle and the salary allocation has been set to 100%. The salary allocation set ensures the salary is captured within the payroll cycles.

2. Does the payroll month match the join date?

Payroll runs in sequence from January. If the employee joined later in the year, the earlier months show no employees — run and complete the empty months first, then continue month by month until you reach the month of the join date.

3. Is the employee included in the payroll cycle?

Being in the payroll center is not enough: the employee also has to be included in the cycle being run. Either check that the employee is assigned to the payroll cycle at the Payroll tab, or click into the ongoing payroll cycle, click on the Edit cycle button and check that the employee has been included in the payroll cycle.

4. Are the statutory bodies enabled for the payroll center?

If no employees appear at all (or the payroll run shows validation warnings), check HR Lounge > Payroll > Settings > General, scroll to Registration Information, tick the statutory bodies that apply (EPF, SOCSO, EIS, HRDF), Save, then refresh the payroll cycle — the employees should now appear in the cycle.

Also worth knowing

  • Subsidiary accounts: users connected from a Main Account into a subsidiary can be excluded from payroll processing there.
  • Deliberately excluding someone: when you are not required to process payroll for a specific employee (for example, paid by a sister company), exclude them from the payroll center rather than leaving them in — see How to Exclude Employees from Payroll.

FAQ

Q: The employee is in the cycle but the basic salary shows 0.
Go to the employee's profile > Payroll > Payroll cycle section: check that the box for the cycle is ticked and the salary allocation is 100% for that cycle.