Speaking at an interfaith event in Abu Dhabi, Most Rev Justin Welby said "It would not be over-stating matters to say that Christianity is both the numerically largest faith and the most persecuted".
In an apparent reference to Donald Trump, Archbishop Justin also warned that a crisis in freedom of religion had "renewed permission for those in political campaigns to condemn all Muslims".
He said it had also allowed politicians to target "other groups they dislike".
Trump has said during his campaign to become president of the United States that he would ban all Muslims from entering the country until they can prove they are not terrorists.
Archbishop Justin warned that freedom of religion "cannot be taken for granted in a world currently beset by a crisis of confidence in the rights it pledged itself to uphold in the aftermath of the Second World War".
He added: "The crisis is affecting all faith groups, deepening nationalist tensions, and leaking across from the approach to faith into the most acute challenges to international law, human flourishing and stability."
Christians in the Middle East have "never felt so threatened", he said.
"Sixty eight years after the United Nations agreed the Universal Declaration of Human Rights, this situation is intolerable and as faith communities we must step up and hold governments to account.
"The right to life is more than just the right not to be killed; it is the right to flourish as fully rounded human beings: body, mind and spirit together.
"Religious freedom is more than just freedom from persecution; it is the freedom to choose how to express our understanding of our relationship with God."
The archbishop closed his speech with a warning that the "increasing integration of Muslim communities within British society" is in "stark contrast to the increasing marginalisation of and outright hostility to Christian communities within many parts of the world, not least in significant parts of the Middle East".
