Surveillance overreach by the US government could have a disastrous long-term effect on internet freedom and free speech, Human Rights Watch warns in its latest report.

The US-based organisation says in its 24th annual survey that there is a danger some governments with poor human rights records, like China or the Gulf states, will use the NSA scandal as an excuse to "force user data to stay within their own borders, setting up the potential for increased internet censorship".

Human Rights Watch's 2014 report is the first in its 36-year history to include a warning about data protection. Previous reports had focused on internet issues mainly in relation to China, where the government has censored internet searches and arrested bloggers who have criticised the government online.

Over the years, China has invested a lot of money in building up the Golden Shield Project, known as the "Great Firewall of China". Last year, the Communist party threatened legal action against people who post on microblogs such as Sina Weibo. Activists fear the NSA scandal will now give China's government an excuse to "nationalise" the Chinese internet completely.

On Monday China appeared to indicate a new, tougher course when it announced that internet users will be required to register their real names to upload videos on the Chinese equivalent of YouTube. The new rule has been implemented, according to a state agency, in order to "prevent vulgar content, base art forms, exaggerated violence and sexual content in internet video having a negative effect on society".

Human Rights Watch director Kenneth Roth told the Guardian that his organisation had chosen to concentrate on data protection because "serious missteps by the US government compelled us to speak up".

"The Snowden revelations have made clear that there has been an intrusion on our right to privacy of unprecedented scope, yet the government is dismissing any complaints about our right to privacy as irrelevant."

Roth said that from a human rights perspective, one of the biggest missteps the US administration had committed was to insist that there was a difference between the content of private communication and "metadata" – information about where, when and between whom the communication takes place. This distinction was based on a 1979 court case from the pre-digital era, which Human Rights Watch described as "troglodyte".

Roth said: "I used to be a prosecutor – I used to put pen registers on people's phones, collecting the numbers that you dial – but I had to manually compile the numbers. It was very labour intensive, and hence self-limiting. Today, the computer can piece together your entire personal life in a matter of seconds."

To assume that only the listening in, not the collection part of surveillance constituted an intrusion of privacy was "a fallacy", Roth said. "Imagine the government putting a video camera in your bedroom and saying 'don't worry, the feed will only go into a government computer, which we won't look at unless we have reason to believe that wrongdoing is taking place'. Would you feel your privacy is being respected? Of course not. But that's exactly what the government is doing."

Human Rights Watch had taken little solace from President Barack Obama's speech last Friday, Roth said. "Obama said there will be no more spying on Angela Merkel. Great! But what concerns us is the US government spying on ordinary people. He didn't say we have a right to privacy. He just said: we'll tread more carefully. What use is the government promising to restrain itself if it doesn't give anyone the chance to challenge that restraint in court?"

As well as covering data protection, the 667-page report also highlights human rights abuses in over 90 countries. Human Rights Watch, which has 16 offices around the world, highlights what it calls a global trend towards "abusive majoritarianism": governments who pay lip service to the principles of democratic rule but discriminate against political minorities. New governments like Egypt or Burma, but also Kenya, Thailand, Turkey, Russia and Ukraine are cited as examples of this tendency.

The report also criticises the "painfully narrow" response to slaughter and suffering in Syria, and singles out Russia for refusing to make use of its considerable leverage to stop atrocities.