Section 100B(2) TMA 1970 specifically excludes the statutory onus of proof (Sections 50(6) to 50(8)) from applying to appeals against penalties. Where there is an appeal against any type of penalty determination, the onus of proof (see AH1320) is with HMRC because HMRC is asserting default.
If an appeal is made against a late filing penalty, the onus is
on HMRC to prove that the return was late. Only once this onus is
discharged it is necessary to consider whether or not the appellant
had a reasonable excuse for the return being late.
Often, the appellant will admit to filing late and claim that he had a reasonable excuse for doing so. In such cases the onus on HMRC to prove that the return was late is discharged by the acceptance by the appellant that the return was late.
Once it is accepted that the return was late, it is up to the taxpayer to show that he had a reasonable excuse, i.e. the evidential burden (see AH1320) shifts to him.
Where you are alleging that the taxpayer is guilty of fraudulent or negligent conduct, then the onus is on you to show that the offence has been committed. If the Commissioners accept that an offence has been committed and a penalty incurred they then have to decide whether to confirm or to vary the penalty (see AH3955). The evidential burden is likely to shift as the parties put forward their contentions regarding the amount of the penalty.