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. I have made a mistake, am I able to correct it and re-finalize my STP for the year?
  3. Am I required to provide a payment summary to the employees?
  4. How do I check to ensure that my EOFY has been successfully submitted?
  5. How do I add Reportable Fringe Benefit Amounts to an employee?
  6. How can I check to see what will be reported for an employee for the year?
  7. STP Payroll gross amounts missing for BAS reconciliations
  8. I need to pay Directors fees, how can I do this?
  9. I have Directors that receive a yearly bonus, how can I pay this to super?
  10. What reports can I use to reconcile my EOFY year?
  11. My employees have advised that their MyGov amounts are incorrect?

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.


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I have made a mistake, am I able to correct it and re-finalize my STP for the year?


Yes, each submission that you make to the ATO will update the employee's balances accordingly and this can still be done if needed after the employees have been finalized for the year.


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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. "


Alternatively, if you or your employees prefer ClockOn provide STP reporting that can be either printed or emailed to the employees from the completion screen on the STP Wizard.



Please note: Employees may 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 finalize their amounts as Tax Ready.


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


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


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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) 


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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 be viewed via the STP Employee Summary report, which can be found under the Payroll Reports > PAYG heading within the report manager as shown below.



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STP payroll gross amounts missing for BAS reconciliations


In the instance where the total gross reported from the ClockOn software product differs from their company's STP business portal, this has occurred due to one or more of the following reasons;

  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 employee's 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.


To check on what has been processed through STP please use the STP Audit Summary report, which can be found under the Payroll Reports (PAYG) heading.


If you have encountered this do not worry, the gross amounts can be manually overridden on the business portal prior to your BAS submission, and we recommend using the the gross amounts from the ClockOn reporting to get the correct values. 


Please note: 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 within the BAS prefill screen.


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I need to pay Directors fees, how can I do this?


To allocate funds for Directors fees you will need to use a before-tax allowance with the STP type set to indicate as such
For an example of the setup for this allowance, please see below.


Once this has been done, you can then set the amount for the allowance from the payroll screen.



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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 directors fees and allocate the allotted amount as a super salary sacrifice.


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What reports can I use to reconcile my EOFY year?


Below is a list of the useful reports that can be run if you require further reconciliation for the EOFY. Run all of the reports of the Current Financial Year when selecting the periods. On the Superannuation report tick all of the Super Reporting Months that fit into the financial year.


PAYG Summary (YTD Adjustments, Compact)

This report will give you all the totals for the financial year and also show any YTD adjustments that have been made in the payroll.


Payroll Summaries – Payroll Allowances/Deductions (Adjustment Roll-up)

For this report select all of the allowances/deductions that are not included in the gross wages and are to be set as allowances on the PAYG summaries. You can then check the allowance amount and also

Superannuation fund summary (Payment type)

This report will show you, by the Superannuation fund, the split of the employer contributions, super salary sacrifice and co-contribution amounts.
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My employees have advised that their MyGov amounts are incorrect?


This can occur in the following instances

  1. You have moved from another STP system to ClockOn and at the time the opening balances were entered against the employees, hence they have been submitted twice.
  2. The BMS (unique id for your business for STP purposes) may have changed mid-year, causing a portion of the employee's payment amount to be duplicated on the ATO's system. 


For the first option, you may need to run a process of reducing each of the employee's YTD amounts as submitted in the previous system and entering the amounts in the YTD Opening Balances section. After this has been complete a re-finalizing the employee's details using the STP wizard will correct this for the employees. 


If the second instance has occurred we recommend either contacting our support team to run a process of reducing the incorrect amount back to $0, or alternatively, contacting the ATO directly to remove the duplicate values.


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