Tim Berners-Lee was speaking at the launch of his World Wide Web Foundation's second annual index measuring the Internet's contribution to social, economic and political development and human rights.
"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," said Berners-Lee.
In 80 percent of the 81 countries surveyed, the Internet and social media played a role in public mobilisation in the last year, the foundation said.
But because some governments are threatened, Mr Berners-Lee says bold steps need to be taken to ensure the fundamental rights of users aren't compromised.
“We should build a system of proper checks and balances," he said.
“Every time we give an agency in government power to break privacy, we need to have another one which is watching it. We [need to] have another system which is powerful, independent and is accountable, as near as we can make it, to the public.”
Australia had mixed results, according to the index. Australia's best showing was in "relevant content, which measures access to information and the provision of government services online. We ranked second behind the UK.
Our worst result was in "Freedom and Openness", which includes the blocking of Internet content and personal data protection, among others. We ranked 30th.
Analysts in Australia say the findings should prompt users to ask more questions about internet surveillance.
“There is a trend towards increasing surveillance of our communications by government online, rather than controlling or reducing that surveillance,” technology analyst Dr Suelette Dreyfus told SBS.
“That's worrying for democracy because it has a chilling effect on free speech.”
Developing countries are most likely to block and filter online communications, but leaks from fugitive US analyst Edward Snowden revealed that developed countries are more likely to spy on the web, the foundation said.
China, Russia, Saudi Arabia and Pakistan are among the worst offenders for censoring politically-sensitive web content and having inadequate safeguards against government surveillance, the report said.
But the United States, Canada, Britain, Australia, New Zealand and India were listed alongside Mali, Yemen and Kenya as having "inadequate" safeguards against government spying.
Sweden topped the overall Web Index for developed countries for the second year running, largely because of the widespread penetration of broadband, followed by Norway, Britain, the United States and New Zealand.
Mexico topped the list of emerging market countries, followed by Colombia, Brazil, Costa Rica and South Africa, while the Philippines was number one among developing nations followed by Indonesia, Kenya, Morocco and Ghana.
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