Multi-EBA Payroll for Contractors Working Across Sites

Multi-EBA payroll works by deciding which agreement applies to each employee, site, classification and shift, then paying the matching rates and clauses from the correct effective date. A site change alone does not automatically change the employee’s EBA.

Start with coverage, not the pay rate

When a worker moves from one project to another, it is tempting to copy the new site rate into payroll and get on with the week. That is where trouble starts.

First ask which industrial instrument legally applies. EBA is the common site term, but the Fair Work Act calls it an enterprise agreement.

An agreement may cover a particular employer, group of employees, occupation, project or location. The wording matters. So do its approval date, nominal expiry date and operation date.

A client’s site agreement does not automatically bind every subcontractor on site. Your business and employees must be covered by it, and the agreement must apply under the Fair Work Act. Site access rules, union arrangements or a commercial contract may create separate obligations, but they do not by themselves decide the employee’s industrial instrument.

As a practical rule, do not let supervisors choose an EBA from a drop-down list without controls. Coverage is a legal decision, not a preference.

You can read more about agreement coverage and common construction clauses in the EBA payroll hub.

Can two EBAs apply to the same employee?

Under the Fair Work Act, only one enterprise agreement can generally apply to an employee at a particular time. Two agreements might appear to cover the work, but payroll still needs a documented decision about which one applies.

That decision may depend on:

• the employing entity
• the employee group named in each agreement
• the work and classification being performed
• the project or geographic scope
• operation and termination dates
• transfer of business rules
• Fair Work Commission orders or determinations

Do not simply choose the agreement with the higher hourly rate. A higher base rate may sit beside lower allowances, different overtime rules or a different rostered day off arrangement. The whole entitlement needs to be considered.

If coverage is genuinely unclear, get workplace relations advice before processing the affected period. Keep the written decision with the employee and site records.

Build a site and employee coverage matrix

A coverage matrix gives payroll one place to check the rule before a timesheet is paid. Here is a basic example.

Payroll question	Site A	Site B	Site C
Employing entity	Contractor Pty Ltd	Contractor Pty Ltd	Civil Works Pty Ltd
Applicable instrument	Company enterprise agreement	Project enterprise agreement	Civil construction award or relevant agreement
Covered employees	Named trades and labourers	Employees performing defined project work	Employees of the civil entity
Rate trigger	Classification and competency	Classification, project and start date	Classification and work performed
Site-specific items	Travel and fares	Project allowance, productivity payment	Distant work or living-away arrangements
Super rule	Percentage of ordinary time earnings	Percentage plus agreement minimum	Instrument clause and statutory minimum
Approval needed for change	Payroll manager	Workplace relations and payroll	Payroll manager

The actual matrix should include agreement titles, Fair Work Commission approval references, operation dates and clause numbers. It should also identify who approved the coverage decision.

Effective dates matter on every site move

Rates and allowances often change during a project. An agreement might contain annual increases, staged increases or a project allowance that starts only after a specified event.

Store each rate with a start date and, where known, an end date. Never overwrite the old rate. You may need it for a retrospective timesheet, backpay calculation or payroll audit.

For each site movement, record:

1. the employee’s last shift at the old site
2. the first shift at the new site
3. the applicable agreement at each site
4. the classification and pay point
5. roster, shift and ordinary-hours pattern
6. site allowances and eligibility conditions
7. the person who authorised the change

If the worker spends one week across two sites, calculate each shift under the applicable rules. Do not average the site rates unless the agreement clearly permits that method.

Keep the pay components separate

A single all-purpose rate can hide mistakes. It becomes difficult to prove whether overtime, allowances, leave and super were calculated correctly.

Keep separate payroll components for:

• ordinary hours
• overtime at each multiplier
• afternoon, night and weekend shifts
• rostered days off and accruals
• site, productivity and disability allowances
• fares, travel time and travel reimbursement
• meal and crib allowances
• inclement weather payments
• leave and public holidays
• redundancy contributions
• superannuation

This is especially important when an allowance is payable for all hours, only ordinary hours or only time physically worked on the project. The agreement clause should drive the calculation.

Check the legal floor as well as the EBA

An enterprise agreement operates alongside the National Employment Standards. It cannot remove minimum NES entitlements.

As at September 2026, the statutory super guarantee rate is 12% of ordinary time earnings, subject to the applicable super rules. An EBA may require a higher contribution, a nominated fund process or a minimum weekly amount. Use the minimum weekly super clause tool when checking how a weekly minimum interacts with part weeks, leave and site transfers.

As at September 2026, the NES maximum for a full-time employee is 38 ordinary hours per week, plus reasonable additional hours. An EBA may arrange those hours across a roster cycle, but payroll must still follow the agreement’s ordinary-hours boundaries.

As at September 2026, full-time employees receive 4 weeks of annual leave under the NES, with 5 weeks for certain shiftworkers. Agreement definitions can affect who qualifies as a shiftworker, so check the clause rather than relying on the employee’s job title.

As at September 2026, Fair Work employee records must generally be retained for 7 years, and a payslip must be issued within 1 working day of payment. Site allocation, hours, rates and allowance records should be detailed enough to explain each amount on that payslip.

Watch for employees who are called contractors

Construction businesses often use the word contractor for both subcontracting companies and individual workers. They are not the same thing.

An employee of a subcontracting company can be covered by that employer’s enterprise agreement. A genuine independent contractor is not put through employee payroll under an EBA. However, calling someone an independent contractor does not settle their legal status.

If the person works under close control, cannot delegate, uses the business’s systems and is paid mainly for their labour, get advice about employee status and sham contracting risk. Do that before deciding which payroll rules apply.

Run a pre-pay comparison

Before finalising each pay run, compare the calculated pay with the employee’s prior week and expected site profile. Large differences deserve a quick look, but small differences can matter too.

Check for:

• workers paid against an inactive agreement version
• missing site transfers
• classification changes without an effective date
• overtime paid using the wrong base
• duplicate site allowances
• minimum weekly super applied twice
• RDO accruals continuing after a roster change
• backpay omitted from leave or super calculations

Think of it like checking the set-out before pouring concrete. Fixing the position early is far easier than pulling apart months of pay runs later.