Representative André Carson, Democrat of Indiana and one of three Muslim lawmakers in Congress, called the citizenship bill “yet another attempt to effectively reduce Muslims in India to second-class citizens.” He said it was the latest attempt by the country’s prime minister, Narendra Modi, to “promote Hindu supremacy” in the world’s most populous democracy.

Under Mr. Pompeo, the State Department has elevated the issue of religious freedom and its role in foreign policy to include for the first time hosting annual meetings of senior foreign diplomats to discuss challenges to faith-based liberty.

“All governments have a duty to protect people from harm regardless of their beliefs, and to hold perpetrators of persecution accountable,” Mr. Pompeo said in August, while the siege in Kashmir was underway. At the time, he cited religious persecution in China, Iran and Myanmar, but not India.

A briefing last month by Sam Brownback, the State Department’s special ambassador for international religious freedom, was notably silent on the plight of Muslims in Kashmir. And in an Oct. 28 speech about Tibetan Buddhism, delivered in India, Mr. Brownback urged governments to protect “religious freedom for all people, everywhere, all the time” — but never once mentioned the anti-Muslim moves by Mr. Modi’s government.

In statements this week, the State Department urged India to “protect the rights of its religious minorities.” It called on authorities to respect peaceful protests against the citizenship legislation and urged demonstrators to refrain from violence. The department also urged India’s government to reopen mosques and shrines in Kashmir that were closed because of the unrest and said it was concerned by restrictions on cellphone and internet access.

Separately, the United States Commission on International Religious Freedom, a federal body, called the new citizenship legislation a “dangerous turn in the wrong direction” and said that the United States should consider sanctions against India.

The citizenship bill and Kashmir are expected to be raised by the United States at the meetings with India’s foreign and defense ministers. But those issues are not the focus of the discussions.