Are Relief At Source Pension Contributions deductible when Calculating Adjusted Net Income

I have receive a notice from HMRC advising that I have underpaid income tax in 2023/4 due to part of my personal allowance having been lost due to my gross income being greater than £100k. I have made pension contributions in the year to a workplace pension scheme which operates under a "relief at source" scheme. These have not been deducted from my gross income as they do not appear on my P60. Am I correct in assuming that these "relief at source" pension contributions should be deducted to calculate my adjusted net income for personal allowance calculation purposes? If so how do I do communicate this to HMRC? Thank you.

Hi,
If the pension contributions are taken from your net income then yes they can reduce your adjusted net income Personal Allowances: adjusted net income.
If deducted from your gross pay before your tax is calculated then you will already have received the relief and would already be taken into account in the adjusted net income. 
Thank you.

Thank you for this confirmation. Can you advise how I would do so, is it via submitting a self-assessment return?

Hi,
If you already submit a Self Assessment return, you can update your return with the pension payments made.
If you are a PAYE taxpayer, we can update your 2023 to 2024 calculation for you.
Please contact our Income Tax team with the figure of pension payments made in 2023 to 2024.
Income Tax: general enquiries
Thank you.