We have had a number of FAQ queries in regards to the processing of EOFY for employee payments through the ClockOn system


Please note that this document relates to frequently asked questions around the ClockOn EOFY system, If you need assistance with how to set this up in your system, please refer to the Processing EOFY through ClockOn knowledge base article.



Included in this document is information regarding the following items:

  1. If I am submitting STP do I still need to upload an Empdupe file to the ATO?
  2. Am I required to provide a payment summary to the employees?
  3. How do I check to ensure that my EOFY has been successfully submitted?
  4. How do I add Reportable Fringe Benefit Amounts to an employee?
  5. How can I check to see what will be reported for an employee for the year?
  6. STP Payroll gross amounts missing for BAS reconciliations
  7. I have Directors that receive a yearly bonus, how can I pay this to super?




1 - If I am submitting STP do I still need to upload an Empdupe file to the ATO?


No, if you have commenced submitting with STP you should not use the EMPDUPE files for the financial year as doing so will report your records twice to the ATO.


If you have done this please contact the ATO to advise so they can correct their records.


Return to top




2 - Am I required to provide a payment summary to the employees?


If you are not yet using STP then you are required to provide the PAYG information to your employees on request, this is done through the PAYG Summary Wizard


You can still choose to provide the paper copy to your employees if you wish however based on advice from the ATO

"If your employer has started reporting through STP, they are no longer required to give you a payment summary. You will instead receive an income statement. You will be able to access this information through your ATO online services via myGov. "


The employees will not be able to start their EOFY process through the MyGov portal until the year-end STP process has been completed as this process is needed to finalise their amounts as Tax Ready.


Return to top




3 - How do I check to ensure that my EOFY has been successfully submitted?


You can check your STP submission status through the ClockOn Message centre, this screen will show you the status of all your previous submissions and if there were issues allow tools for troubleshooting issues. 


Return to top




4 - How do I add Reportable Fringe Benefit Amounts to an employee?


Please see the following help guide for how to add RFBA into the system for your employees
Adding any Reportable Fringe Benefits (RFBA) 


Return to top




5 - How can I check to see what will be reported for an employee for the year?


As with STP ClockOn will report the details as per the employee's YTD records, these can viewed via the Employee year-to-date and Employee Year-To-Date (Compact) reports which can be found under the Payroll Reports > PAYG heading within the report manager as shown below.



Return to top




6 - STP Payroll gross amounts missing for BAS reconciliations


We have had some customers report that the total gross reported from the ClockOn software product differs from their company's STP business portal.


This screen was designed to record each STP payroll submission as a line item and the total gross associated with it. Issues can arise from this in the event that there has been one of the following

  1. Payroll submission events were missed. If this is the case do not worry as the employee's STP details will be up-to-date if you have successfully run an STP submission or update event after this point.

  2. A payroll was submitted to STP, then rolled back and reprocessed to correct payroll values as this will result in a miss-match with what was submitted and the ClockOn reporting.

  3. YTD adjustments through the ClockOn payroll system, as these adjustments will update the employees YTD earnings without directly influencing the payroll.

    For example, a YTD before allowance will not attract tax or super, and as these amounts do not affect the payroll directly they are not included in the gross amount and as such will not be reported within the payroll amount.


If you have encountered this do not worry, the gross amounts can be corrected on the business portal end prior to your BAS submission and you can use the gross amounts from the ClockOn reporting to get the correct values. 


Please note that the employees will have the correct amounts within their MYGOV accounts based on what has been processed through the system regardless of what is shown on this screen.


Return to top



7- I have Directors that receive a yearly bonus, how can I pay this to super?


Please refer to the Superannuation Employee and Employer Payments for instructions on how to pay either an additional bonus amount or catch up on the required SGC amount.


Return to top