EM6305 | Contract Settlements: Letters of Offer: Penalty-Only Offers
From HM Revenue & Customs · Enquiry Manual
The guidance about contract settlements at EM6000+ only relates to direct tax. You must never include VAT or VAT penalties in a contract settlement.
Contract settlements are a mutually-beneficial administrative convenience. They replace what we would otherwise do formally: a single exchange of letters instead of a raft of closure/amendment/assessment/determination notices.
There may be occasions when a combination of the two is the most cost-effective way to settle. For example, if any enquiry covers one year only it might be more convenient to
close and amend formally
let the SA system attend to the interest
cancel any SA surcharge on tax to which the penalty is geared - S59C(4) - and
make a contract settlement for the penalty only. Letter 12
You should seek advice from Contact Link as necessary on the appropriate wording in less straightforward cases.