VCP11141 | Breach of VAT Regulatory Provisions: Definition of Regulatory Penalties: Discretion
From HM Revenue & Customs · VAT Civil Penalties
Regulatory penalties are assessed under the VAT Act 1994 Section 76 and as such are discretionary. You therefore have the discretion whether or not to assess for a penalty.
Having established the liability to the penalty you then need to decide if a penalty assessment should be made. When making this decision you will need to make sure you apply fair and equal treatment, taking
full account of the circumstances of the particular case, and
not forgetting that the fundamental objective of the penalty is to deter non- compliance.