There is a special rule that allows you to include the minimum 3% KiwiSaver Company Contribution in the employee's pay, by having a special clause in their employment agreements. This means the employee’s salary or wage covers the cost of the company’s KiwiSaver contribution.
For example, a $60,000 salary would normally have 3% paid on top for the KiwiSaver Company Contribution. However, with the special clause in this case, the 3% is included in the $60,000.
How to Enable This Setting
Please head over to "Company Settings", then select "Payroll Settings".
Open "Advanced Settings", then open "KiwiSaver, Superannuation & SWSAS Settings".
Tick "Turn on Advanced Options for KS or superannuation".
Click "Save".

How to Use This Setting
When setting up "KiwiSaver" in "Employee Settings", then "Employee Details", choose "Advanced Options" and tick "Use employee salary sacrifice to cover company contribution".

When you process the pay, the company contribution will be deducted from the pay as a pre-tax deduction, as shown below:

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