I have an employee who has been sponsored by the company, he was on a 417 Visa until January 2024, and he was granted a 482 visa during this time the immigration department was still awaiting a police check, they then pushed the employee onto a bridging visa for the 482 pending the police report from Germany. The employee did a self-assessment online with the ATO that recommended he is now a resident for tax purposes, and he lodged a tax declaration form with us to change is ATO status. We acted on the tax declaration form provided by the employee and changed his status and taxed him accordingly.
The employees tax agent is now telling him that he is not required to lodge a tax return, and the employer has withheld the incorrect tax amounts and that they should return this money to him direct.
can you please clarify what status the employee should be on ?