The Treasury has concluded last-minute negotiations with the BBC and will restrict its borrowing limit to £230m, instead of the £400m the corporation was seeking.
The new limit is part of the overall licence fee settlement, as part of which the annual payment will rise to 3% over each of the next two years and a maximum of £151 by 2012.
He also welcomed the longer settlement at six years, enabling efficient planning for digital switchover, rapidly changing audience expectations and new creative initiatives.
Thompson said: "Our vision for the future, broadly endorsed by a government White Paper, as well as their own requirements and ambitions, especially around digital switchover, plus not wanting existing, valued BBC services to be squeezed as we invest for the future, led us to bid for a settlement that would increase in real terms.
"The settlement announced today means the BBC still receives substantial, guaranteed income of more than £20bn over the next six years, which is financial security denied to any other media player. But it leaves a gap of around £2bn over the next six years between what we believed we needed to deliver our vision and what will actually be available."
The BBC said its executive board and senior managers across the organisation would now review investment plans in the light of the settlement and explore the options.
The executive will then make initial recommendations to the BBC Trust ,which will make decisions later in the year in the best interests of licence fee payers, drawing on the framework of the BBC's public purposes and public value.
Thompson said: "The BBC faces challenges to find enough money to create the fantastic content our audiences want.
"After seven years of funding that has grown in real terms, we now face not just a tight settlement but daunting investment challenges in distribution, infrastructure and technology that risk diverting money away from content creation.
"These challenges call for some new thinking about how we produce content and how we create value."
Thompson said that the BBC's vision for content in the digital world, 'Creative Future', was never fundamentally about spending new money. "It is about flexing, adapting, liberating all content, but above all, content we already make. It's about unlocking the full value of existing investment."
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