Generating Employee Payment Summaries


At the end of each financial year, one of the tasks payroll administrators start preparing for is generating individual non-business payment summaries (aka group certificates) for their employees.

The good news is, what was previously a time consuming process, can now be completed in a few simple clicks by following these steps:

NOTE- Electronic submission of payment summaries will not be allowed when payee address details are incomplete, or when they have supplied an invalid TFN.

  1. Log in and ensure that all pay runs have been finalised for the current financial year.  

  2. Once all pay runs and housekeeping tasks have been finalised, click on the 'Reports' menu and under the 'ATO Reporting' section, click on the 'Payment Summaries' link:

  3. From the payment summaries screen, select the financial year you wish to generate payment summaries.

    N.B. If you have multiple employing entities set up in your account, ensure you filter by entity accordingly.

  4. You can then click on “Show Payment Summaries” to generate payment summaries for all employees in the business or chosen employing entity.

  5. If you see the following message on your screen, take note that the payment summaries will still generate but will not include wages data contained in unfinalised pay runs so we strongly suggest you finalise all pay runs prior to continuing further.

  6. Once your payment summaries are generated you can download an excel report that contains all data displayed on your screen. This is a great report to use to ensure all data is reconciled and figures are correct prior to publishing payment summaries. To generate this report, click on "Excel".
  7. To view a single payment summary, click the 'Actions' menu next to a particular employee, then click 'Download'.

  8. Once you are happy with the payment summaries, you can publish them by clicking on 'Actions', then 'Publish x payment summaries'.
  9. To preview all published payment summaries, click on "PDF".

10. Lodge your payment summaries (with the ATO) - if you haven't set up electronic lodgement with the ATO yet just click here to see an article that will step you through this process.


NOTE: If any new pay runs are created for that financial year or any changes are made, the payment summaries must be re-generated for any changes to take effect. 

How do I enter the Reportable Fringe Benefits amount?

Once the payment summaries are generated, you are able to enter the Reportable Fringe Benefits (RFBA) amount. To do so, click the 'Actions' button next to the payment summary and click 'Edit'.

The Reportable Fringe Benefit Amount (RFBA) field is open to enter in a dollar amount.

Please ensure you:

  1. Enter the "grossed-up" taxable value of these benefits;
  2. Do not enter any cents; and
  3. Do not include this amount in the "Gross Payments" field.

You may need to seek advice on which FBT deductions are reportable. Further information on FBT can be found here.

How do I change the payment period on a payment summary

You can change the payment period for a payment summary by following these steps:

  1. Ensure the payment summary has not been published
  2. Click on the "Actions" -> "Edit" button on the payment summary you want to change the payment period for

  3. The payment period dates are now editable. Enter in the dates for the payment period and click 'Save'

What happens when I publish payment summaries?

Once you publish the payment summaries, they become available to the employees for download via the self-service portal. If you would like to send the employees an email notification to let them know that their payment summaries are generated, click the 'Send Notifications' button. 

What if I need to change the values in the payment summaries after I’ve published them

There are two options available:

  1. You can unpublish an individual payment summary by clicking on the Actions button next to the relevant employee and then “Un-publish”.

  2. You can unpublish ALL payment summaries by clicking on 'Actions' (top menu)  button and then “Un-Publish x payment summaries”.

Once you have unpublished the payment summaries, they will no longer be available for download by employees in the employee self service portal.

You can now make any necessary changes to the pay runs or create a new pay run, then re-generate the payment summary/summaries. If you have already issued the payment summaries to the employees/ATO, you may need to mark the new payment summaries as 'Amended'. To do this, click the check-box when generating the payment summaries:

You may then republish the payment summaries by clicking on the "Publish" button.

If it's just one payment summary that you want to make changes to go ahead unpublish it by choosing this option on the Actions button for that payment summary...

Then, once it's unpublished click on the Actions button again but this time choose the Edit option...


The following areas are the only sections you are able to "edit" on the payment summary itself - changes to earnings and other aspects must be made in the pay runs...

Republish the payment summary from the Actions button and "Lodge" it again - if you are making changes to several, but not all, payment summaries, follow the process outlined above and then hit the Lodge button here...

Only payment summaries that have been marked as Amended will be "re-lodged".

Can EMPDUPE files be generated for the ATO?

Yes (although this is not required if you "lodge" the payment summaries)! To find out more about generating EMPDUPE files click here.

If you have any questions around generating PAYG payment summaries, please let us know via

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