In September, HMRC collected £34m, an increase of 62% from a low of £21m collected in May.
Tax investigations were suspended during the start of the lockdown as it shifted many of its investigations staff into helping taxpayers with emergency coronavirus assistance, which resulted in a slump in penalties being imposed on taxpayers.
The total amount taken in from penalties fell 36% from £730m to £468m in the year to 30 September 2020.
Sean Glancy, VAT partner at UHY Hacker Young, said: “The lull in HMRC investigations is largely over. Many accountancy firms are already reporting an increase in HMRC enquiries so if you do have tax that you have avoided or evaded then now is the time to come forward.
“The first deadline on amnesty for businesses that overclaimed furlough payments ended on October 20 and HMRC have so far identified 27,000 high risk cases.”
He added: “Businesses that have not come forward under the furlough amnesty should be braced for HMRC to impose the highest penalties that it can.
“This is exactly the kind of area that HMRC will deliberately impose tough penalties to create a deterrent effect.”