In an annual report, the US Commission on International Religious Freedom also raised concerns about what it called a worsening situation in China, as well as problems in Egypt, Iran, Myanmar, Saudi Arabia and other nations.
The commission, which advises the government but does not make decisions, called for the US to designate Pakistan as a "country of particular concern," meaning it could be subject to sanctions if it fails to improve.
Assessing the year through January 31, the commission said religious freedom violations in Pakistan "rose to unprecedented levels due to chronic sectarian violence" that targeted the Shiite Muslim minority.
Sunni Muslim extremists over the past year have killed hundreds of Shiites in Pakistan, especially Hazaras -- a community originally from Afghanistan that is known for its comparatively liberal attitudes.
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"Pakistan is in a crisis right now with these particularly severe violations of religious freedom," said Knox Thames, the commission's director of policy and research.
The commission, whose members are appointed by President Barack Obama and Congress, said Pakistan faced the most serious violations of religious freedom among any country not already on the blacklist.
The designated countries of particular concern on religious freedom are China, Eritrea, Iran, Myanmar, North Korea, Saudi Arabia, Sudan and Uzbekistan.
Along with Pakistan, the commission urged the State Department to add Egypt, Iraq, Nigeria, Tajikistan, Turkmenistan and Vietnam to the list.
The report said that religious freedom in China "deteriorated significantly" in the past year, especially for Tibetan Buddhists and Uighur Muslims, but also for followers of unauthorised churches and the banned Falungong movement.