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."