Judge Geraint Jones threw out the case against Peter Jacks, who HMRC claimed had filed a late return.
But HMRC had been unable to prove that the taxpayer had been sent a notice to file and could only produce a computer printout which showed the taxpayer’s name and a date of issue.
Judge Jones said: “Adequate proof is a necessity; not a luxury.
“We do not consider that we can be, or should be, satisfied, on the balance of probabilities, that a notice to file was posted by an officer of HMRC to the appellant simply based upon the computer held note ‘Return Issued Date’ alongside which appears ‘6/4/15’.
“Even if the notice to file was issued on 6 April 2015 there is, quite literally, no evidence or even any note to the effect that it was dispatched to the appellant at a specified address.
“That is a fundamental link in the chain upon which liability to a penalty depends.”
Mr Jacks was appealing against a late filing penalty imposed on him in respect of the alleged late filing of his self-assessment tax return for the fiscal year ended 5 April 2015.
The penalties levied amount to £1,200 being made up of £100 for not filing by 31 January 2017, £900 being the daily penalty for 90 days at £10 per day and then £300 because the return was not filed after six months had elapsed.
Andrew Hubbard, a tax consultant with RSM, said he had a feeling of “déjà vu all over again” in relation to HMRC’s failure to provide evidence.
He said: “We are seeing more and more tax appeals where the burden of proof plays a key part in the decision.
“It may sound an academic or abstruse concept but it is vitally important. Citizens’ rights against the state need to be vigilantly protected.”
He said HMRC should not put its head in the sand about this issue, adding that there were only two ways of addressing it: radically changing the way documents and correspondence are created and stored, or reversing the burden of proof by law.
He said: “That would be a fundamental shift in the balance of power and would be something we would very strongly resist.
“HMRC needs to get its house in order and not throw the problem in the direction of the taxpayer.”
Figures show that HMRC's decisions are upheld by the tribunal in 83 per cent of all appeal cases.