Over-declaration of Import VAT

Hello,
I would like to enquire about an over-declaration of import VAT.
A company imported two items in a single consignment (valued over £135).
However, the attached invoice covered the full order from their UK customer, which listed three items.
As a result, import VAT was paid on all three items with the first consignment, even though the third item was imported into Great Britain at a later stage and subject to import VAT again.
This has led to an over-declaration of import VAT, which is reflected on their C79 certificate.
My question is:
Can the company reclaim the over-declared import VAT as input tax on their VAT return, given that they hold the corresponding C79 and paid the import VAT?
Or should they contact their customs agent to rectify the over-declaration?
Thank you.

Hi Rainer,
If you’re a VAT registered business, you’ll need to make an adjustment through your VAT return, following normal VAT rules. Overpaid import VAT is not due to HMRC so you cannot recover it as input tax.
To claim a repayment you’ll need to:
• reduce the amount of output tax due in Box 1 of the VAT return
• keep an audit trail to support your claim
Please see guidance at:
How to claim a repayment of import duty and VAT if you've overpaid
Thank you.