Religious freedom has deteriorated in Iraq and Egypt, while China has cracked down on foreign missionaries ahead of the Olympics, the US government said.
Conditions in Iraq worsened after an attack on a shrine in Samarra
The annual State Department report on religious freedom said violence in Iraq was not suffered by just Shia and Sunni Muslims, but all religions and sects.
Burma, Eritrea, Iran and North Korea were also criticised for their treatment of religious minorities.
The report noted signs of improvement in Saudi Arabia, India and Vietnam.
Religious freedom in Saudi Arabia was still severely restricted, but the government had tried to foster greater tolerance by public discussions and announcements, the report said.
Hatred and intolerance
Religious freedom is "integral to our efforts to combat the ideology of hatred and religious intolerance that fuels global terrorism," said US Secretary of State Condoleezza Rice as she unveiled the report.
The 800-page document said the freedom to worship in Iraq had sharply deteriorated over the past year, despite the US military build-up.
All religions were victims of "harassment, intimidation, kidnapping and killings", the report stated, citing the ongoing insurgency as a "significant" factor.
Ms Rice did not refer to Iraq directly but said the report, covering 198 countries, was integral to President George W Bush's efforts to promote religious freedom worldwide.
In neighbouring Iran, the US said that there was a threatening atmosphere with harsh and oppressive treatment of all religious minorities.
In Egypt - a key US ally - respect for religious freedom had "declined" - while the constitution provided for freedom of belief, the government restricted those rights, the report said.
In China there "credible reports of deaths due to torture" involving the Falun Gong spiritual sect, as well as expulsions of foreign missionaries, the report said.