130,000 taxpayers were taken out of the self-assessment process when HMRC's updated their records to simplify the tax system this year. 12,000 of them have received the penalty notice by mistake.
HMRC has apologised for the error and confirmed that recipients do not have to do anything and will not be out of pocket.
An HMRC spokesman said: "We have identified that nearly 12,000 people have been sent a self-assessment daily penalty letter in error. We are very sorry and can reassure these customers that we know who they are and that this letter is incorrect - they do not owe a penalty. We are writing to all of them to apologise and to explain this error.
"The 12,000 customers are among the 130,000 who we have already taken out of self-assessment, following a cleanse of the database and our invitation to customers to contact us if they felt they shouldn't be in self-assessment. We can reassure these customers that they have been removed from self-assessment.
"It is very unfortunate that this process error has taken the shine off the good news that we have taken 130,000 people out of self-assessment."