Deputy director Anne Bulford said loans and advances had been given after some were told to set up personal service companies so they could be treated as freelancers.
The move saved BBC beancounters millions in National Insurance contributions. But presenters lost employment rights such as holiday and sick pay and pension contributions.
Tax chiefs then tightened the rules and presenters had to pick up the tab. Ms Bulford told the Commons Public Accounts Committee: “We are talking about comparatively modest sums in the overall scheme of things but important to the individuals. We think it is the right thing to do.”
She said she could not rule out the BBC ending up paying some of the back taxes too.
BBC Director General Lord Hall said: “HMRC have said the test which they were asking us to apply is not fit for purpose so we need to have yet another test.
“This has caused a good deal of confusion for individuals — a great deal of anger among the people who are our frontline presenters, mainly in radio and in news.
"In some cases it has caused some hardship.
"My sympathies are to the people who are on the raw end of this.”
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