US allies including Saudi Arabia and Bahrain did not uphold principles of religious freedom in 2016, while the Islamic State of Iraq and the Levant (ISIL, known as ISIS) group has carried out "genocide" against religious minorities, Secretary of State Rex Tillerson said.

Tillerson made the comments on Tuesday at the Department of State while introducing the agency's annual report on religious freedom, required by a 1998 act of Congress.

The report is the first to be released during the Trump administration and covers 2016.

Saudi Arabia, Tillerson said, ought to "embrace greater degrees of religious freedom for all of its citizens".

He cited criminal penalties for apostasy, atheism, blasphemy, and insulting the Saudi state's interpretation of Islam, as well as attacks and discrimination targeting Shia Muslims.

The kingdom follows the Sunni Muslim Wahhabi school of Islam.

The report said Saudi Arabia has used counterterrorism laws to target atheists and Shia Muslims.

The United States and Saudi Arabia have long been close partners in fighting groups like al-Qaeda and ISIL.

Riyadh was the first stop on President Donald Trump's maiden international visit earlier this year.

READ MORE: Saudi Arabia executes Shia men for 'violent attacks'

Tillerson singled out another Gulf Arab country, Bahrain, saying it "must stop discriminating against the Shia communities".

In Turkey, a NATO ally, "authorities continued to limit the human rights of members of some religious minority groups," Tillerson said.

American pastor Andrew Brunson has been jailed in Turkey since October on charges of being part of a terrorist organisation, according to news reports.

Tillerson said religious freedom is "under attack" in Pakistan, citing the marginalisation of Ahmadiyya Muslims, a minority sect which Pakistan considers non-Muslim.

Tillerson said ISIL "is clearly responsible for genocide against Yezidis, Christians, and Shia Muslims in areas it controls or has controlled".

Iran, China, Sudan named

He also said Iran targeted religious minorities including Baha'is and Christians, and in 2016 executed 20 people on charges including "waging war against God".

China and Sudan were also singled out in his remarks.

The Chinese government tortures and imprisons thousands for practising their religious beliefs, Tillerson said, citing the targeting of Falun Gong members, Uighur Muslims and Tibetan Buddhists.

In Sudan, the government arrests and intimidates clergy and blocks the construction of churches while tearing down existing ones, he said.

READ MORE: China Uighurs - Ban on long beards, veils in Xinjiang

Tillerson's decision to introduce the report contrasted with how he handled the Department of State's annual human rights report in March.

He declined to unveil it in person, breaking with precedent and drew criticism he was not giving rights issues adequate attention.

The report did not address Trump's attempt this year to temporarily suspend refugee admissions and his decision to impose a lower cap on the number of those admissions.

The report states that resettlement is a "vital tool for providing refugees protection".

Many refugees admitted to the US in 2016 were fleeing religious intolerance and persecution, it said.