The waste management group said the amount relates to a single biomass customer and is part of the £40.4m of disputed landfill tax assessments which the firm paid in full in December 2019.
The company stated the reimbursement will be treated as an “exceptional profit” in the businesses results for the year ending 31 December 2020.
It is also believed that Augean intends to seek interest and costs from HMRC.
In addition, the industrial firm also awaits the decision of another “more significant” element worth approximately £16m of the disputed landfill tax from the first tier tax tribunal which was heard in September 2020.
Jim Meredith, executive chairman of Augean, said: “The group is pleased to have received notification of HMRC’s repayment. Nonetheless, it is disappointing that the process with regard to this small element of the overall claim has taken more than three years to reach the right outcome.
“Based on legal advice received, we continue to maintain our position that we have correctly collected and paid the appropriate landfill tax throughout, and we will continue to robustly challenge the disputed remaining assessments that have been paid in full through the tax tribunal system.”
Accountancy today has contacted HMRC for comment