How Payroll fields link to ATO income statements – Employment Hero Australia

When an employee sees more than one income statement in myGov, it does not always mean their income has been reported twice.

The Australian Taxation Office (ATO) uses identifying information submitted through Single Touch Payroll (STP) to organise an employee’s payroll records. Different reporting details can result in separate income statements, even when the employee works for the same business, or their earnings are processed in one Employment Hero Payroll file.

This article explains which Payroll fields affect income statements, why multiple statements may appear, and how to correct incorrectly duplicated earnings.

How does the ATO identify a payroll record?

The ATO uses a combination of four key identifiers:

Employer ABN.
ABN branch number.
Business Management Software (BMS) ID.
Employee STP Payroll ID.

Employee identity details, including their TFN, name and date of birth, also help the ATO match the information to the correct person.

Having the same employee name and TFN does not automatically combine records reported under different payroll identifiers.

Check the financial year as well. Income statements for different financial years are separate records.

Which Employment Hero fields relate to these identifiers?

The following locations apply to Employment Hero Payroll classic.

Field	Where to check in Payroll	How it relates to the ATO record
Employer ABN	Payroll Settings → Business Details and ATO Settings. For an additional employing entity, check Payroll Settings → Employing Entities → the relevant entity.	Identifies the employer the earnings were reported under. Earnings reported under different ABNs can appear on separate income statements.
Branch number / branch code	Payroll Settings → ATO Settings. For an additional employing entity, check that entity’s settings.	Identifies the reporting branch under the ABN. Different branches can create separate records, even when the ABN is the same.
BMS ID	Payroll Settings → ATO Settings → Electronic Lodgement & STP. For an additional employing entity, check that entity’s BMS ID.	Identifies the payroll reporting source. Reporting under a different BMS ID can create an additional income statement, depending on the transition process used.
STP Payroll ID	Employee profile → Opening Balances → STP. The default is the employee’s Employee ID shown on their Details screen.	Identifies the employee’s payroll record within the reporting source. A new employee profile or an incorrectly matched migration ID can result in a separate record.

Important: The BMS ID and Software ID are different fields. When comparing income statement identifiers, check the BMS ID.

Not all identifiers may be visible on the employee’s income statement screen, these are shown on the PDF version of their Income Statements.

Why can an employee have more than one income statement?

They were paid under different ABNs or branches

An employee may move between employing entities during the financial year.

For example, they earn $30,000 under Entity A and $20,000 under Entity B. They may have:

Income statement	Earnings reported
Entity A	$30,000
Entity B	$20,000
Combined earnings	$50,000

These statements can both be correct. Each represents the earnings reported under the relevant employer.

A branch change can also result in separate statements under the same ABN.

The business changed payroll systems

A payroll migration may involve a different BMS ID or employee STP Payroll ID.

Depending on the transition option used, the employee may have separate statements for earnings reported from the previous and current systems.

The important check is whether the earnings are correctly split between the statements or whether historical earnings have been included on both.

The employee has more than one payroll profile

Creating a new employee profile can generate a different STP Payroll ID.

Even if both profiles have the same employee name and TFN, the ATO may receive them as separate payroll records.

Reporting details were corrected after STP was lodged

If earnings were first reported under an incorrect ABN, branch number, BMS ID or STP Payroll ID, changing the field in Payroll does not automatically correct the information already held against the previous record.

The historical record may also need an STP correction using the identifiers originally reported.

How can I tell whether the statements are correct?

Check the earnings as well as the number of statements.

Situation	Statement 1	Statement 2	What this means
Earnings correctly split between two employers or reporting sources	$30,000	$20,000	Combined earnings are $50,000. Both statements may be valid.
Earlier earnings also included in the second statement	$30,000	$50,000	Combined earnings are $80,000. If actual reportable earnings are $50,000, the earlier $30,000 may have been reported twice.

These examples use simplified earnings amounts. When reconciling actual records, also compare PAYG withholding and the relevant STP payment categories.

What should I check?

Confirm the financial year. Compare statements and Payroll reports for the same year.
Review each income statement. Note the employer ABN, employee number, amounts and finalisation status.
Compare the reporting identifiers. Check the ABN, branch number, BMS ID and STP Payroll ID used for each reporting source.
Review changes during the year. Include payroll migrations, employing entity transfers, branch changes and newly created employee profiles.
Reconcile the amounts. Compare each statement with the earnings that belong to that reporting source, then check the combined totals.

Check historical lodgements as well as current settings. The values currently saved in Payroll may differ from those used when an earlier STP event was lodged.

How do I correct an incorrectly duplicated income statement?

If the same earnings have been reported against two different payroll records, the general correction logic is:

Reset the incorrect record using its original identifiers, then report the correct earnings against the correct record.

This process applies where the entire incorrect record needs to be cleared. If a statement contains valid earnings as well as incorrect amounts, follow the applicable correction guide to retain the valid earnings.

*** Important *** If you have any additional employing Entities you will need to ensure that the employees are on the correct entity when actioning these steps.

Step 1: Identify which record needs correcting

Compare both income statements with the employee’s payroll history.

Confirm:

Which record contains incorrect or duplicated earnings.
Which record should contain the earnings.
Whether either statement contains valid earnings that must remain reported.

Multiple income statements can be valid. Only reset a record where the earnings should not have been reported.

Step 2: Match the identifiers used for the incorrect statement

The earnings reset event must use the same identifiers that were used to report the incorrect income statement:

Employer ABN.
Branch number.
BMS ID.
Employee STP Payroll ID.

Select the financial year that needs correcting.

All four identifiers must match the original record. If you lodge the reset using the current identifiers instead, it will target the current record rather than the incorrect historical record.

You may need to temporarily restore the original reporting settings and the relevant employee employing entity assignment. Follow the correction guide for your scenario before changing these settings.

Step 3: Lodge the earnings reset event

Lodge the earnings reset event for the affected employee against the incorrect record and confirm the lodgement is successful.

Where the entire record is incorrect, the reset reports zero employee year-to-date (YTD) amounts against that combination of identifiers. Follow the relevant guide for any required Mark as Final selection.

An earnings reset corrects the STP figures reported to the ATO. It does not reverse the employee’s actual pay.

Step 4: Restore the correct settings and report the correct earnings

Once the reset has been successfully lodged:

Restore the correct ABN, branch number, BMS ID, STP Payroll ID and employing entity assignment, as applicable.
Check that the employee’s earnings are allocated correctly.
Lodge an update event to report the correct employee YTD figures, or an amended finalisation if the relevant record has already been finalised.

The reporting event must use the identifiers belonging to the correct record.

Step 5: Check the result

After the ATO processes the corrections, check that:

The incorrect record no longer contains duplicated earnings.
The correct record contains the expected earnings and PAYG withholding.
The combined income statement totals reconcile with the employee’s reportable payroll figures.
The finalisation status is appropriate for each record.

The aim is to correct the amounts reported. A reset does not guarantee that the ATO will remove the additional statement from view.

Example: Incorrect branch number

An employee’s earnings were initially reported under branch 007, then reported again under branch 005.

Branch 005 is correct, and the same earnings appear on both statements. No earnings should remain under branch 007.

Action	ABN	Branch	BMS ID	STP Payroll ID
Reset the incorrect record	Original ABN	007	Original BMS ID	Original Payroll ID
Report the correct earnings	Correct ABN	005	Correct BMS ID	Correct Payroll ID

Resetting under branch 005 would target the correct record. To clear the incorrect earnings, the reset must target branch 007, using the other identifiers originally reported.

Important: If earnings were legitimately reported under branch 007 for part of the year, do not reset the entire statement to zero. Retain those valid earnings and follow the applicable correction process.

Will an update event automatically fix both statements?

An update event reports employee YTD information against the identifiers included in that event.

An update event using the current identifiers does not automatically clear earnings reported under different, previous identifiers.

For example, lodging an update event under the correct branch number can update that record, but it does not clear earnings previously reported under an incorrect branch number.

The incorrect record needs its own correction using the identifiers originally reported.

Why does Payroll show one total while myGov shows two statements?

A Payroll report may show an employee’s combined earnings across the file, depending on the report and filters selected.

The ATO organises income statements using the STP reporting identifiers. A combined Payroll total therefore does not necessarily correspond to one income statement.

Where multiple employing entities are involved, use the relevant entity filters, where available, and compare the STP information reported for each entity.

Will these corrections update employer-level BAS totals?

Update events correct employee YTD information. They do not update employer-level gross payments or PAYG withholding totals used for BAS W1/W2 pre-fill.

If the correction also affects employer-level totals, review the relevant activity statement separately. You can manually correct the relevant W1/W2 amounts on your activity statement with the ATO.

What information should I provide if I need help?

If the statements do not reconcile or you cannot identify the original reporting details, provide:

The Payroll business URL and affected employee profile URL.
The financial year.
Screenshots showing each income statement’s employer details, employee number, amounts and status.
The current and previous ABN, branch number, BMS ID and STP Payroll ID, where known.
Details and dates of any migration, entity transfer or reporting changes.
The relevant STP lodgements and any corrections already completed.

Mask the employee’s TFN in screenshots.

This information helps identify whether the statements represent valid separate earnings or whether an earlier reporting record needs correcting.