The corporation released the information as a response to a freedom of information request by The Sun newspaper.
However, the report did not include the bonuses paid to the BBC's top 10 executives, who were collectively paid a total of £232,000 in bonuses according to last month's BBC annual report.
A spokeswoman for the BBC said: "The BBC pays small bonuses in recognition of good performance. These are one-off payments and are not salary increases. The majority of bonus payments made to staff in the past year were less than £1,000.
"The total paid out in bonuses comes from the BBC's budgeted staff costs, which are published each year in the BBC's annual report. These are separate from programme costs."
The bonus payments to staff are awarded to individuals on a discretionary basis, a move that has angered broadcasting union Bectu. Three unions - Bectu, NUJ and the Musician's Union - are currently in negotiations with the BBC to avert strike action.
Gerry Morrison, Bectu general secretary, said that the union was opposed to selective bonus payments for employees. He said: "We would always prefer that the process is transparent, and in this case it doesn't seem to be.
"We would call for any bonuses paid by the BBC are not simply awarded to individuals but across the board in a consolidated bonus scheme for all staff."
The dispute focuses on the 2006 2.6% pay offer to BBC employees, a figure 0.4% below the current 3% inflation rate, which the unions have rejected.
A ballot for strike action was due to be called on August 3, but is understood to have been averted by BBC director-general Mark Thompson, who held a closed-door session with unions last month.
The unions are due to meet on September 1 to discuss the issue further.
The BBC spokeswoman, added: "Bonuses are given at the discretion of line managers and this system helps to ensure the BBC can attract and retain the best staff. This practice is in line with pay policies of other media organisations and most major companies."
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