The department sent out the letter to 1,500 individuals, with 700 thought to have reached intended recipients over the weekend.
While the majority of individuals and businesses will remain unaffected, HMRC is keen to show that it is cracking down on tax avoidance after recent headlines on the subject.
The BBC quotes the letter as saying: "You are in the small minority of people who have made the deliberate choice to avoid tax. We focus our resources on this small minority. The choice that you have made changes the way we view your tax affairs."
It adds that the Specialist Investigations Unit will be looking into one avoidance scheme in the coming months.
Last week, Essex businessman Patrick Larkin was jailed for two years after being found guilty of VAT fraud following a HMRC investigation.
Posted by Emily Smith