The corporation continued paying hundreds of employees after they left their jobs, and has also been overpaying some existing staff - to the tune of around £75,000 a month last year.
However, it has launched proceedings to claw back all the known overpayments and is confident it will retrieve most of the funds.
“We action recovery of every overpayment, and expect to recover the full amount in almost every case. This process is common within industry where there is a high turnover of taxable contract and fixed term workers,” a spokesman said.
According to BBC figures, as of last November former staff still owed £698,000 from the 2007/08 financial year; £394,000 from 2006/07; and £234,000 2005/06 - a total of £1.3m over three years.
Existing staff owed a further £200,000 from 2007/08; £164,000 from 2006/07; and £69,000 from 2005/06 - giving a three-year total of £433,000.
However, the BBC said that the actual size of the outstanding debts is much lower because the official figures do not wipe debts until they are paid off in full.
In reality, the funds are usually collected in instalments meaning that many affected staff and former staff will be mid-way through repayments. In the case of current BBC staff, the funds are automatically deducted through payroll.