Seaman’s Tax

I’ve been working as a seaman for the last 15 years. Firstly for a U.K. company following a PAYE system where tax deducted monthly and if I reached the required days I could claim seaman’s tax exemption. I then worked 8 years via an agency that if I didn’t reach the sea days then I was responsible for the tax. I now directly work for the company as permanent employee who is from Luxembourg but with a U.K. office. I have a net contract and I’m responsible for filling in my self assessment but if I’m required to pay tax they will pay but if I got a refund through seaman’s tax deduction then I’m required to give this back to company. Could you confirm if this is correct or not? Kind regards.

Hi,
Any agreement on who pays the tax or gets a refund is between you and your employer.
Guidance on seafarers is at Seafarers Earnings Deduction: tax relief if you work on a ship
Thank you.