In an email to staff today, Thompson announced he would not be accepting his £135,000 bonus saying it was inappropriate considering the job cuts.
"I took a personal decision to waive my own right to a bonus this year. As the architect of our change programme, which is only just getting under way and which has led to a great deal of uncertainty for many of you, I thought I was in a different position from the other directors," he said.
In the BBC's annual report unveiled today, chairman Michael Grade announced that a bonus of 30% of an executive's base salary figure was too high for a publicly funded organisation because BBC salaries should be based on the market median.
"We concluded that it was important to retain some element of performance-related bonus, but that 30% was too high for a public sector organisation," he said.
The corporation also revealed that while programming spend had increased by £101m throughout 2004/2005 on its main terrestrial channels, audience share has fallen.
BBC One was down 1.8 percentage points to an 81.9% weekly reach while BBC Two fell the hardest -- down 5.6 points to 61.4%.
BBC Digital channels were up on audience figures, with BBC Three, home of 'Little Britain', up 2.4 points to 9.4% of the weekly digital reach and BBC Four was up 0.9 points to 3%.
However, the corporation ploughed £325m into its digital channels, far exceeding the top performing digital channel ITV2, which only receives £25m from the ITV network.
BBC Radio performed slightly better, with Radio 1 and Radio 2 up 0.2 points and 0.5 points respectively. Radio Five Live was also up 0.2 points to a weekly reach of 12.7%. BBC Radio 3 and Radio 4 were down 0.3 points and 0.5 points respectively.
In total, the BBC made £2.94bn from licence fee payers, up £142m from the previous year, and reduced its public service debt by £17m to £89m.
The BBC's commercial activities, including its magazines, books and licensing divisions, brought in £151m for the year, up £16m on 2003/2004.
In addition, the BBC also said it spent £8.4m on its governance unit, but refused to give a breakdown on how the money was spent.
The corporation will enter into Charter Renewal negotiations with the government this autumn. As it stands, the BBC has only secured a promise that it will be funded by the government for the next 12 years.
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