Please note that the STP process has replaced the need for this guide, this functionality is only to be used to produce PAYG summaries for financial years prior to 2021.

For the current process for submitting your EOFY to the ATO please see the Processing EOFY through ClockOn article.

Please be aware that this process will NOT submit details though STP.

ClockOn provides functionality for Employers to generate PAYG summaries for employees to complete their EOFY process with the ATO. To produce these summaries please follow the steps below;


To open the Wizard select the Payroll tab and click on Create PAYG Summaries option.

Proceed through the wizard as per the steps below;

  1. Set the following based on your submission requirement, and click Next to continue;
    • Location - You will need to run this for each location that has a different ABN.
    • Financial Year Ending - Indicates the financial year that you are generating the reporting for.
    • Amendment - This is used if you are re-submitting the EMPDUPE01 file to the ATO for the financial year.

  2. Step 1: Verify your location details. 
    If this is incorrect you will need to Close the EOFY Wizard and correct these values in the Location Manager.

  3. Step 2: Verify your contact name and click on Next to continue

  4. Step 3: Employees to consider for YTD rebuilding.
    This screen will show any employees who have had manual changes made to their Employee YTD values and hence they no longer the same as what has been recorded at the time of payroll.

    Please note that the ideal is for none of your employees to show on this list as this means that all matched as expected.

    You have the option to:
    1. Ignore: The system will use the balances from the employee's YTD page and ignore the payroll processed amounts.
    2. Rebuild: The system will override the amounts within the YTD screen based on what was processed through ClockOn.
    3. Restore: This is used after a rebuild has been completed for an employee and you wish to revert back to the manual changes that were made.

  5. Step 4: RSEC 
    This screen scans over the employee's payslips to check for where employees had any super that meets the RSEC requirement such as super above the SGC amounts (as set in the employee's Ruleset) or Salary Sacrifices amounts. 
    1. Select the employees to include and click the Calculate button to retrieve the employer contribution for the financial year. These amounts will show on the RSEC Column.
      NOTE: Manual changes to the employees YTD’s will show in the RSEC column, prior to pressing the calculate button, and will not be recalculated when you click on the calculate button. If you want to recalculate these figures to be what was processed at payroll, tick the include box and then the calculate button.

  6. Step 5: Employees to Include 
    This is the list of employees that will be included in the creation of the file to be submitted to the ATO as well as your PAYG and ETP summaries.

    NOTE: Employees that are deselected are those that did not pass the validation check. to find out why or correct any employees you will need to cancel the wizard and re-run the validation wizard (as above)

    The Aggregate column advises of any employees who have 2 or more card files, and the values for each will be contained within a single document. This will occur if the employee card files share the same:
    1. Location ABN
    2. Title, First, and Last Name
    3. TFN
    4. Date of Birth

  7. Select the file location of where you want to save your EMPDUPE01 file required to upload to the ATO. To do this click on the yellow folder icon and you will be prompted with a window to Choose a folder when where the EOFY data will be saved. By default, the file location will be in the ClockOn installation folder on your computer.

    When the file is created it will be created under the selected folder called EOFY\LocationName\FinacialYearEnding 
    (example: C:\Program Files (x86)\ClockOn\EOFY\Malvern Entity 001\2018\EMPDUPE.A01)

    Note: This screen is only avaliable if a STP submission has not been processed for the ABN

  • Step 7: Printing the reports.
    On the final page of the wizard, you will have to option to Print and Email the Individual PAYG Summaries and ETP Summaries.

    For each type of summary, you will have the options to:
    1. Print all of the employee summaries.
    2. Print only the employee summaries who don’t have an email address in their card file
    3. Email all the employee summaries who have an email address in their card file.
      TIP: If you are unsure if you have any ETP summaries try printing them first before just emailing them.

Click on Finish to close the wizard.

TIP: You can run the Create PAYG Summaries wizard as many times as you need to check that all is reconciliation is correct. just be aware that by doing this the EMPDUPE01 file will be over written each time you run it. So the final time you run the wizard will be the one you upload to the ATO.