Hello, I am Keith, one of the experts on Jast Answer, and pleased to be able to help you with your question.
Which tax form are you using? Is it the long or the short version. You should be claiming on a Form R40.
You don't use R40. If you are registered as a non-resident landlord, you are automatically put into the self-assessment system. The tax deducted figure goes into box 21 on the property income page UKP2 here. See the note on box 21 in the notes on page UKPN4 here.
If you are completing the return using the HMRC software, you should find the box for the tax deducted figure in the UK property income section.
I hope this helps but let me know if you have any further questions.
Unfortunately the system does not always work correctly. I have clients in a similar situation who are being sent R40s. In theory you can get HMRC to issue a tax coding to give you your personall allowance if you are entitled. All EEA citizens are entitled to this allowance.
I can't be bothered to argue as its late in the UK but I don't believe for one minute registered non-resident landlords are being sent R40s. I've been in tax and only tax for 37 years and I don't subscribe to the "man down the pub told me to do it this way" philosophy. I use the system put in front of me, the proof of which is in the links I gave you. Some others choose to use their own rules which can only lead to trouble. Why fight a system that works?
Your calculation clearly doesn't show the tax deducted by the letting agent. You need to find the box in the software you are using. Are you using the HMRC online tax return software or a third party commercial software? The HMRC software allows you to submit an amended return as do the commercial software products. You have until 31 January 2017 to amend your 2015 tax return.
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You should definitely take it up with your accountant, he only appears to be doing half the job.