New VAT Penalty regime

From 1 April 2022 a new penalty system will apply for both late VAT return submissions and late payments.  It will also apply to other taxes although our focus is VAT.

The intention behind the new system is to be fairer. It will achieve this by penalising the few taxpayers who persistently fail to meet submission obligations rather than those who make occasional mistakes. It is important to note that one impact of the new regime will be that repayment traders will also potentially be liable to penalties if they submit their returns late.

The new penalty regime is described as being akin that used in relation to traffic offences in that it is ‘points based’. Points will be given when a business defaults and when a certain number of points have been incurred penalties will apply.

Details of how the new late submission penalty system will operate can be found on HMRC’s website. However, the main points to note are summarised below.

Late submission

Taxpayers will receive a point every time they miss a submission deadline. HMRC will notify them of each point. At a certain threshold of points, a financial penalty of £200 will be charged and the taxpayer will be notified. The threshold is determined by how often a taxpayer is required to make their submission.

When a taxpayer has reached the relevant threshold, as determined by their submission frequency, a penalty will be charged for that failure and every subsequent failure to make a submission on time, but their points total will not increase.

The penalty thresholds will be as follows:

Submission frequencyPenalty threshold
Annual2 points
Quarterly4 points
Monthly5 points


Points will have a lifetime of two years; after which they will expire. This will be calculated from the month after the month in which the failure occurred. Points will not expire when a taxpayer is at the penalty threshold. This ensures they must achieve a period of compliance to reset their points.

After a taxpayer has reached the penalty threshold, all the points accrued within that points total will be reset to zero when the taxpayer has met both the following conditions:

  • A period of compliance (that is, meeting all submission obligations on time for the period of compliance – see table below); and
  • The taxpayer has submitted all the submissions which were due within the preceding 24 months. It does not matter whether or not these submissions were initially late.

Both requirements must be met before points can be reset.

The periods of compliance are:

Submission frequencyPeriod of compliance
Annual24 months
Quarterly (including MTD for ITSA)12 months
Monthly6 months


If a taxpayer is at the penalty threshold and has achieved the period of compliance, but has outstanding submissions, they will remain at the penalty threshold and continue to be charged penalties for any further failures to make submissions on time.

Businesses should ensure, prior to the implementation of the new regime, that all outstanding VAT returns have been submitted as any returns that remain outstanding could impact on the penalty position moving forward.

Once a taxpayer has reached the relevant threshold and a penalty has been charged, every subsequent late submission will incur a penalty, but the taxpayer’s points total will not increase.

Late payment

The new Late Payment Penalties will apply to payments due from VAT businesses. Details of how this system will operate can be found on HMRC’s website. The new system will replace the Default Surcharge, which currently serves as a combined late submission and late payment sanction, effectively meaning that only payment businesses were likely to be penalised for failing to submit VAT returns in a timely manner. The separation of the two penalties means a business can be penalised if it is late submitting a VAT return that records a payment due from HMRC (a repayment return), this would not previously have been the case.

There are two late payment penalties that can be applied:

  1. First Penalty for late payment

The taxpayer will not incur a penalty if the outstanding tax is paid within the first 15 days after the due date. If tax remains unpaid after Day 15, the taxpayer incurs the first penalty. This penalty is set at 2% of the tax amount outstanding after Day 15.

  1. Additional or Second Penalty for late payment

If tax remains unpaid on Day 31, the taxpayer will begin to incur an additional penalty on the tax that remains outstanding. It accrues on a daily basis, at a rate of 4% per annum on the outstanding amount. This additional penalty will stop accruing when the taxpayer pays the tax that is due.

Reviews and appeals

A taxpayer will be able to challenge a point or penalty through both an internal HMRC review process and an appeal to the courts (the First Tier Tax Tribunal).

The grounds for an appeal will include the grounds that the taxpayer had a reasonable excuse for missing a filing deadline. The appeals process will be the same as that for a VAT assessment.

Interest Harmonisation

Alongside the introduction of new penalties HMRC is to change the interest regime for VAT to ensure interest is consistently and automatically charged and paid in all cases where amounts are paid late or where amounts have been overpaid, bringing VAT in line with other tax regimes.

After 1 April 2022 HMRC will charge Late Payment Interest (LPI) on tax that is outstanding after the due date, irrespective of whether any Late Payment Penalties (LPPs) have also been charged. The LPI will apply from the date the payment was due until the date on which it is received by HMRC. LPI will be calculated as simple interest at a rate of 2.5% + the Bank of England base rate.

Where a taxpayer has overpaid tax, HMRC will pay Repayment Interest (RPI) on any tax due to be repaid (the difference between the amount due and the amount paid) either from the last day the payment was due to be received or the day it was received, whichever is later, until the date of repayment. RPI will be paid at the Bank of England base rate less 1% (with a minimum rate of 0.5%).

Payment of RPI will replace the repayment supplement currently paid when HMRC does not make a repayment within 30 days. There are concerns that this could lead to delays in HMRC making repayments as the financial impact for HMRC will be less. HMRC has stated that action has been taken to ensure that the repayment team will continue to make repayments promptly and within the time-limits wherever possible.

These new penalties are a significant change to the VAT system. If you wish to discuss the impact on your business please contact us.