This led to Rangers commentators, including ex-player and manager Ally McCoist, insisting that without the taxman's "blunder" the club would not have faced administration and liquidation in 2012.
HMRC has since refuted the article. Their official Twitter account sent out a tweet late on Thursday evening where they insisted they "did not miscalculate anything".
Now chief executive and first permanent secretary Jim Harra has written to the editor of The Times to give their side of the story.
The letter was posted on Twitter. It read: "I am writing in relation to your coverage of Rangers' tax affairs on 14 November 2019. The article is incorrect: HMRC did not make any mistakes that led to the club's insolvency.
"HMRC won against Rangers' tax avoidance in the Supreme Court. We have a long-standing claim with the liquidators to recover the money due as a result of this judgement.
"The United Kingdom has one of the lowest rates of unpaid tax anywhere in the world. Inaccurate and partial reporting only serves to undermine public trust in the tax system.
"HMRC is committed to getting tax right, for everyone - adn to challenge tax avoidance wherever we find it. We make sure large businesses, like all other taxpayers, pay the taxes due under UK law."