Any pay resulting in
negative tax value cannot be processed through a normal pay run, as IRD require you to amend the records previously sent for that employee.
The common reason for a negative pay would be an
overpayment and you are reversing out the hours or allowances paid by using negative quantities. If you have discussed this with the employee and you have
recovered the money they received into their bank account, run an
Adjust a Previous Pay to reflect the change in Year to date earnings for this employee. Tax and KiwiSaver deductions will be refunded also.