We have had a number of FAQ queries in regard 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:
- What reports can I use for reconciling my EOFY figures?
- How can I adjust my Rate sets for award rate increases?
- If I am submitting STP do I still need to upload an Empdupe file to the ATO?
- I have made a mistake, am I able to correct it and re-finalize my STP for the year?
- Am I required to provide a payment summary to the employees?
- How do I check to ensure that my EOFY has been successfully submitted?
- Why is there a mismatch between my STP payroll amounts and my BAS reconciliations?
- How do I add Reportable Fringe Benefit Amounts to an employee?
- How can I check what will be reported for an employee for the year?
- I need to pay Director fees, how can I do this?
- I have Directors that receive a yearly bonus, how can I pay this to super?
- What can I do if my employees have advised that their MyGov amounts are incorrect?
- Can I split my payroll so some ends in the current financial year and the remainder is processed in the new year?
What reports can I use for reconciling my EOFY figures?
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.
Please note that there will likely seem to be an initial difference between the STP and payroll reported figures as the STP reporting will provide a breakdown of the gross into its various components; STP allowances, Paid parental leave, workers compensation, and overtime are some examples.
More information, as well as examples on the usage of these reports, is contained within the ClockOn EOFY webinar of which a link can be found on our Processing EOFY through ClockOn article, starting from at timestamp of approx around the 11:13 into the video.
How can I adjust my Rate sets for award rate increases?
Ratesets allow you to add a minimum award rate that the system will check at the time of your payroll, to advise you as to if they are being paid at least this hourly amount for their work performed.
For more information on how to use Ratesets please see the following guide. Rates Manager
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.
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.
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.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.
Why is there a mismatch between my STP payroll amounts and my BAS reconciliations?
If your total gross reported from the ClockOn software product differs from the company's STP business portal, this has likely occurred due to one or more of the following reasons;
- 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.
- A payroll was submitted to STP, then rolled back and reprocessed to correct payroll values as this will result in a mismatch between what was submitted and the ClockOn reporting. You can see the history of this by running the STP Audit report and it will show instances where the STP information was provided but then removed from ClockOn.
We are not able to remove STP-processed amounts from the ATO's system. - YTD adjustments through the ClockOn payroll system, as these adjustments, will update the employee's YTD earnings without directly influencing the payroll and thus will not be included in the gross and tax submission amounts.
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.
The ATO advises that you use the figures from your payroll system as a primary source over the BAS prefill information.https://www.ato.gov.au/businesses-and-organisations/hiring-and-paying-your-workers/single-touch-payroll/ato-payg-withholding-pre-fill-for-activity-statement
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)
How can I check 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.
I need to pay Director 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.
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.
What can I do if my employees have advised that their MyGov amounts are incorrect?
This can occur in the following instances
- 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.
- 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 completed, re-finalizing the employee's details using the STP wizard will update the MyGov information 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.
Can I split my payroll so some ends in the current financial year and the remainder is processed in the new year?
IMPORTANT NOTE: Consideration needs to be taken before doing this as the ATO bases this on the date that the actual payments were madehttps://www.ato.gov.au/businesses-and-organisations/hiring-and-paying-your-workers/payg-withholding/payg-payment-summaries#Endoffinancialyearpaymentstoemployees
Yes, this can be easily done using the Edit Period button from the Payroll screen.
Set the End Date to the date that you intend to split the payroll to, in the example below we are setting it to 30/06/2024, once set click the Save button to confirm the change.
Process the payroll as normal, ensuring that the payment date is in the correct year.
IMPORTANT: Remember that the Payment date indicated at the commencement of the payroll will advise the system on the financial year that the payroll will be included within. Once the payroll has been run, you can change the remainder of the previous payroll as an additional split payroll. Doing this will keep your current payroll cycle
If this is done we recommend noting that if there is any cumulative overtime that the employees would have been entitled to in the normal period it will need to be managed using Special Rates. When setting the rate, remember to set the STP Type to Overtime to ensure the amount is reported to the ATO correctly.