The latest CITB report and accounts for the year to March 31 2022 contain details of the blunder.
The training body receives cash from the Education and Skills Funding Agency (ESFA) for apprenticeship training based on the number of apprentices it is helping.
But an ESFA audit of CITB apprenticeship number submissions for the 2020/21 period has resulted in a request for repayment of £1.6m and sparked a probe into payments for the two previous years which has forced the CITB into setting aside a provision of £5.9m.
A CITB statement said: “Provision has been made to allow for the potential repayment, if any is due, to the Education and Skills Funding Agency (ESFA) to allow for audit results from 2020-21 and discussion is still ongoing between CITB and ESFA on this.
“This relates to possible historic administrative activity not sufficiently meeting funding requirements. Since then we have put in place several improvements to address this, working alongside ESFA, and these improvements have been acknowledged by ESFA.
“The potential repayment in the report is to cover a number of years should it be needed.”
“It is also important to highlight that this possible administrative issue has not affected the outcomes of Apprenticeship training”.
Current CITB chairman Peter Lauener is a former chief executive of the ESFA.