Loans and advances had been made to 15 people with “temporary financial difficulties”, the corporation’s deputy director-general Anne Bulford told MPs.
She said the sums involved were “comparatively modest in the overall scheme of things but important to the individuals”.
The disclosure came after a Commons committee heard last month that presenters were pushed by the BBC into setting up “personal service companies”, depriving them of employment rights and saving the corporation £10m a year in national insurance contributions.
The presenters were subsequently left with large bills for unpaid taxes after the arrangements fell foul of HM Revenue and Customs.
Former Look North host Christa Ackroyd was the only presenter to be dismissed over the controversy.
She was left with a bill of up to £400,000 after losing a legal battle with HMRC but was later cleared of wrongdoing by a tribunal.
Director-general Lord Hall blamed the problems, which he said had caused a “good deal of confusion”, in part on policy changes by the tax authorities. Lord Hall said the problems – affecting mainly radio and news presenters – were in part the consequence of a series of changes by HMRC as to the way such staff should be treated for tax.
“HMRC have said the test which they were applying and asking us to apply is not fit for purpose so we need to have yet another test,” he told the committee.
“This has caused a good deal of confusion for individuals. It has caused a great deal of anger among the people who are our front-line presenters, mainly in radio and in news.
“In some cases it has caused some hardship. If there are cases of hardship we have made it clear we want to deal with those as a priority. My sympathies are to the people who are on the raw end of this.”
Ms Bulford did not rule out the prospect that the BBC would end up paying the back taxes of some of the staff concerned.
“I can’t conclude on that until we start to work through the individual cases,” she said.
Ms Bulford also denied that managers at Capita, the firm which collects the TV licence fee for the BBC, were being offered cash incentives to maximise the prosecutions. The Daily Mail reported that managers were given generous bonus payments for encouraging door-to-door officers to fill out as many “prosecution statements” as possible.