The corporation has teamed up with three other organisations to launch a licensing system in a bid to get round the rights issues.
Computer users will be able to sign an online agreement pledging not to use the clips for commercial purposes. A BBC source admitted monitoring the licences would be difficult, and said the corporation would not be "actively policing" the system during its trial run, but would take legal action if it found clips being used commercially.
Channel 4, the British Film Institute and the Open University have also signed up to the 18-month pilot scheme, and more organisations are expected to sign up. Together they will form Creative Archive, which is set to become the UK's biggest media store.
The system will give downloaders free reign to use and alter the clips, and there are plans to allow the revised versions to be loaded back onto the website for other users to see.
Natural history and factual will be the first BBC genres to be put online, but it could be months before the clips are made available.