Online surveillance is undermining people's confidence in the internet, warns Sir Tim Berners-Lee – though he predicts that its outcome will be to enshrine users' rights in the longer term.

But he added that whistleblowers such as Edward Snowden, who triggered a raft of disclosures against the US National Security Agency and the UK's GCHQ surveillance agencies, were important: "I think we must protect them and respect them," he said at the launch of a new index showing web freedoms around the world.

Berners-Lee, 58, the British inventor of the world wide web, said: "One of the most encouraging findings of this year's Web Index is how the web and social media are increasingly spurring people to organise, take action and try to expose wrongdoing in every region of the world. But some governments are threatened by this, and a growing tide of surveillance and censorship now threatens the future of democracy"

He also said that those who have revealed secret surveillance deserved praise: "Countries owe a lot to whistleblowers – there's a series of whistleblowers who have been involved. Snowden is the latest. Because there was no way we could have had that conversation without them.

"At the end of the end day when systems for checks and balances break down we have to rely on the whistleblowers – I think we must protect them and respect them."

Jimmy Wales, co-founder of Wikipedia, said that as a result of the revelations about surveillance, the collaborative online encyclopaedia will begin encrypting communications with its users all over the world so that people cannot be spied on as they access information.

He said that the revelations of the extent of surveillance and data collection by western governments – such as the arrangement between GCHQ and the NSA that let the US spy agency "unmask" Britons' data – was having a damaging effect on the west's reputation.

"I do hear a lot of concerns about the direction that a lot of governments are taking with respect to the web," Wales said at the same event. "One of the things that I do is campaign in authoritarian countries to explain why it's important for their economies and futures to have freedom of expression online. But when I'm meeting a minister in China or Kazakh, and saying that they're on the wrong side of history, it's important to be able to point to the UK or US as examples. And when I say that they shouldn't be spying on everyone in China or Kazakh, it rings a little hollow. We may trust GCHQ to not take activists away in the night, but if they monitor everybody's communications, then the Chinese will feel justified in doing the same."

Encrypting connections to Wikipedia should make it impossible for surveillance systems to monitor what people are looking up or editing by tapping connections, although it might be possible if the user's computer has been compromised.

Berners-Lee said that the focus of what "freedom" means online had shifted in the past two years, from questions of sites being censored, to fears about governments pulling the plug on connectivity, to new ones about silent surveillance.

"Initially there was peoples' pushback against censorship and websites being blocked, or the internet being just turned off," he said. "Now this spying is a more insidious force which has a chilling effect, where people don't use facilities that they could have used because of a nameless fear of something happening to them."