Urgent advice required - PAYE Tax issue

[JoeLawerence2]

Hi guys, I applied for Naturalisation a couple of weeks before and did my biometrics last Wednesday. Yesterday I got a letter from HMRC stating I paid too less tax for last financial year (2016/17). I applied for my ILR last year and got the £2375 reimbursed from my employer. HMRC have stated this as a 'Benefit in Kind' and have taxed it at £953. Now I have two questions in this regard:

1) Are the HMRC right in taxing me for the visa fees?
2) If yes, and if I pay the tax now, will it affect my naturalisation application?

Very wrong timing to get this letter from HMRC

Thanks in advance for your support guys!

[CR001]

1) Are the HMRC right in taxing me for the visa fees?

It isn't really visa fees. You received an income/bonus/payment from your employer likely through PAYE, so yes, it is taxable.

2) If yes, and if I pay the tax now, will it affect my naturalisation application?

It should not affect your application if you pay it or set up a payment plan.

The simplest thing would have been to get a company cheque for your ILR application.

[JoeLawerence2]

Thanks CR001 for your prompt response.

If I pay tax through the online HMRC portal, will that be sufficient? Or should I call HMRC and make them aware that I have filed a Naturalisation application and so make a note on my records that this has been paid. I am asking this as I am aware that HMRC records take a while to be updated.

[CR001]

HMRC have nothing to do with your naturalisation and wouldn't care either way.

If you pay it, they update their systems.

[JoeLawerence2]

Thanks CR001