The rises also coincided with a fall in its number of viewers. The BBC's total weekly reach dropped from 86.6 per cent last year to 85.3%.
The director-general Mark Thompson saw his pay packet rise by £160,000 from £459,000 to £619,000 although his salary for the previous year was not for a full year.
His fellow executives also enjoyed significant pay rises.
Thompson waived his right to receive a bonus, although his colleagues did not.
The director of television Jana Bennett was paid £353,000 inclusive of benefits and bonus. Her basic pay rose from £255,000 to £321,000.
Jenny Abramsky, director of radio and music, saw her basic pay rise from £233,000 to £295,000 - taking her total wage to £322,000 with benefits and bonus.
Deputy director-general Mark Byford was the best paid executive after Mark Thompson.
His total take-home pay was £456,000, including a basic wage of £403,000 - up from £351,000 the previous year.
The increases come at a time when the corporation is cutting costs and axing jobs.
Some 1,132 posts have already been closed, with more than 2,000 to go next year.
The BBC said the pay hikes were part of a two-year process to bring executives' base pay up to the market median.
While base pay has risen, bonus potential has been reduced from 30 per cent to 10 per cent.
BBC chairman Michael Grade said: "The governors believe the BBC's executive pay policy now properly reflects our combined duty to licence fee payers and our responsibility as employers."
The audience figures were also revealed in the Corporation's annual report today. Flagship channels BBC1 and BBC2 appeared to suffer the biggest casualties.
The weekly reach for BBC1 was 79.7 per cent, down from 81.9 per cent last year, while BBC2 was at 59.1 per cent, slipping from 61.4 per cent.
The figures measure the percentage of people who watch BBC TV for at least 15 minutes in an average week.
Digital channels BBC3 and BBC4 measured healthier performances this year than in previous years: BBC3 up to 16.1 per cent from 14.8 per cent last year and BBC4 to 6.1 per cent from 4.8 per cent last year.
The figures were unveiled in the BBC's annual report, which comes as the Corporation prepares to learn whether it will receive the 2.3 per cent licens fee rise above inflation that it has asked for, which will take the figure to an estimated £180 by 2013.
The BBC will argue that the drop in viewing figures is being experienced by all broadcasters and is a consequence of the explosion of digital channels.Reuse content