Heiner Bielefeldt, the UN Special Rapporteur on freedom of religion or belief, said there was too much focus on the use of criminal law in areas such as blasphemy, apostasy and forced conversion.
He warned that many other ways were being used to harass individuals and communities because of their faith.
There is an "increasingly challenging environment for security and freedoms", he suggested in a speech to the UN General Assembly.
Some Christians were suffering extra bureaucracy and administrative requirements that people of other religions didn't face.
Many countries had family laws and education that discriminated against people of certain faiths, he warned.
"Religious intolerance does not directly originate from religions themselves," said Bielefeldt. "Human beings are the ones ultimately responsible for open-minded or narrow-minded interpretations."
He said that in some cases hate crime and violence against others was actively supported and encouraged by Governments.
"Often, authoritarian Governments are obsessed with controlling all types of religious activities, on the pretext of promoting harmonious relationships between the political party and the people," he said.
"Questioning this 'harmony' is a taboo, as the Governments fear the monopoly of the party itself will be challenged."
He warned that in countries where the state was failing, terror groups and vigilantes were taking over and leading to an increase in persecution.
Andreas Thonhauser from religious freedom group ADF International told Premier's News Hour: "There are cases of persecution that might not include the most henios crimes like killing and torture and rape but are still a harassment because people believe in Jesus Christ.
"We believe that no person should live in fear because of their religious beliefs."
Andreas Thonhauser speaking to Premier's Antony Bushfield:
