How to Create a BAS Lodgement for Healthcare & Allied Health
A comprehensive procedure for preparing, reviewing, and lodging the Business Activity Statement with the Australian Taxation Clinic, covering GST, PAYG withholding, PAYG instalments, and other obligations.
Purpose
To ensure that the organisation Business Activity Statement is prepared accurately and lodged on time, consultation all GST, PAYG withholding, and PAYG instalment obligations while minimising the risk of penalties and interest.
Scope
Covers the preparation of quarterly or monthly BAS including GST calculation, PAYG withholding reconciliation, PAYG instalment calculation, and any other applicable obligations reported on the BAS.
Prerequisites
- All transactions for the BAS period have been entered and reconciled in the accounting system
- Bank reconciliations are completed for the BAS period
- Payroll has been finalised for the BAS period with PAYG withholding totals available
- Access to the ATO Business Portal or tax agent portal for lodgement
Includes safeguards for Australian Privacy Principles (APPs), Medicare compliance, and health record management under the My Health Records Act. All patient data handling follows AHPRA guidelines.
Step-by-Step Procedure
Reconcile GST Accounts
Reconcile the GST collected (output GST) and GST paid (input GST) accounts in the general ledger for the BAS period.
- 1.1Run the GST detail report from the accounting software for the BAS period
- 1.2Reconcile GST collected to the sales and income transactions for the period
- 1.3Reconcile GST paid to the purchase and expense transactions for the period
- 1.4Investigate and resolve any transactions with incorrect or missing GST codes
Review GST on Specific Consultation Types
Review GST treatment for specific consultation types that are commonly miscoded, including capital purchases, entertainment, motor vehicles, and imports.
- 2.1Check that capital asset purchases have the correct GST treatment
- 2.2Review entertainment expenses for any GST claiming restrictions
- 2.3Verify GST on imported goods matches the customs import declaration
- 2.4Confirm that GST-free and input-taxed supplies are correctly classified
- Maintain a reference list of common GST-free and input-taxed supply types for quick review
Calculate PAYG Withholding
Reconcile the total PAYG withholding from payroll for the BAS period and confirm it matches the payroll system records.
- 3.1Extract the total PAYG withholding from the payroll system for the BAS period
- 3.2Reconcile the payroll PAYG total to the PAYG withholding liability account in the general ledger
- 3.3Include any withholding from payments to contractors without ABNs
- 3.4Resolve any discrepancies between the payroll system and the general ledger
Calculate PAYG Instalment (if applicable)
Determine the PAYG instalment amount for the period using either the instalment amount method or the instalment rate method as applicable.
- 4.1Confirm which PAYG instalment method the organisation uses
- 4.2If using the instalment amount method, confirm the ATO-advised amount
- 4.3If using the instalment rate method, calculate instalment income and apply the rate
- 4.4Consider whether to vary the instalment if current-year income is significantly different
Prepare the BAS Workpaper
Compile all BAS components into a comprehensive workpaper that supports each label on the BAS form.
- 5.1Complete the BAS workpaper template with GST amounts for labels 1A, 1B, and all other applicable labels
- 5.2Enter the PAYG withholding total at the relevant label
- 5.3Enter the PAYG instalment amount at the relevant label
- 5.4Calculate the net amount payable or refundable
Review and Approve the BAS
The Finance Manager reviews the completed BAS workpaper and supporting reconciliations before authorising lodgement.
- 6.1Review the BAS workpaper for accuracy and completeness
- 6.2Cross-check key figures to the general ledger and payroll reports
- 6.3Compare the current BAS to the prior period for reasonableness
- 6.4Sign off on the BAS and authorise lodgement
- Flag any significant movements from the prior period for additional investigation before lodging
Lodge the BAS
Submit the BAS to the ATO via the Business Portal, tax agent portal, or accounting software integration.
- 7.1Log into the ATO Business Portal or tax agent portal
- 7.2Enter or upload the BAS figures for each applicable label
- 7.3Review the summary and confirm all figures are correct
- 7.4Submit the BAS and save the lodgement confirmation
Process Payment or Refund
Arrange payment of any amount owing to the ATO by the due date, or monitor for a refund if applicable.
- 8.1If an amount is payable, arrange payment via BPAY, direct debit, or EFT before the due date
- 8.2Record the payment in the accounting system against the GST and PAYG liability accounts
- 8.3If a refund is expected, monitor the bank account and record when received
- 8.4Reconcile the ATO integrated patient account to the general ledger
Archive BAS Records
File the BAS workpaper, lodgement confirmation, and all supporting documentation for audit and ATO retention requirements.
- 9.1Save the BAS workpaper, reconciliations, and lodgement confirmation to the BAS folder for the period
- 9.2Retain all supporting consultation reports, payroll summaries, and bank reconciliations
- 9.3Ensure records are retained for at least five years from the date of lodgement
Quality Checkpoints
Common Mistakes to Avoid
Expected Outcomes
The BAS is lodged by the due date every period with zero late lodgement penalties.
Fewer than one ATO amendment or adjustment is required per financial year, indicating accurate preparation.
GST and PAYG liabilities are forecast and included in cash flow planning to avoid payment surprises.
Frequently Asked Questions
Do we need to report Taxable Payments Annual Report (TPAR) data on the BAS?
TPAR is a separate annual report, not included in the BAS. However, businesses in certain industries must lodge a TPAR annually reporting payments made to contractors. Check whether your industry is covered by the TPAR regime.
Can we vary the PAYG instalment amount?
Yes, you can vary the PAYG instalment if you expect your current-year income to be significantly different from the amount used to calculate the instalment. However, penalties may apply if the variation results in a significant underestimation.
What happens if we discover an error after lodging the BAS?
Minor errors can be corrected on the next BAS within certain ATO thresholds. For larger errors, a formal revision of the original BAS may be required through the ATO portal.
When is the BAS due for lodgement?
For quarterly lodgers, the BAS is due on the 28th day of the month following the end of the quarter (e.g., 28 October for the July-September quarter). If the organisation uses a registered tax agent, extended due dates may apply.
What is the difference between cash and accrual GST reporting?
Under the cash method, GST is reported when payment is received or made. Under the accrual method, GST is reported when the invoice is issued or received, regardless of payment timing. Most businesses with turnover above $10 million must use the accrual method.
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