WASHINGTON (Reuters) - The United States is voicing concern over reports from human rights groups that Pakistan’s security forces are holding thousands of political separatists without charge, The New York Times reported on Thursday.

Citing a State Department report to Congress last month, the Times said the Obama administration was alarmed by reports that separatists, mostly from Pakistan’s Baluchistan province, had been detained over the past decade and were being held incommunicado.

Some of the missing were guerrillas and others civilians, the newspaper said. The State Department report, obtained by the newspaper, also cited concerns that Pakistan’s military had killed unarmed Taliban insurgents instead of putting them on trial.

The report urged Pakistan, an important U.S. ally in the fight against Islamist insurgents, to address the issue and other rights abuses, the paper said. “There continue to be gross violations of human rights by Pakistani security forces,” the report said.

“The Pakistani government has made limited progress in advancing human rights and continues to face human rights challenges.” Pakistani intelligence officials accuse human rights groups of exaggerating the numbers of people held incommunicado, according to the Times.

The United States in late September asked Pakistan for information about a video posted on the Internet purporting to show men in Pakistani military fatigues lined up in a firing squad shooting bound and blindfolded men in traditional clothing.

The Pakistani government has launched a probe into the video.

The United States in October announced $2 billion in military aid for Pakistan, but the relationship has been strained by Washington’s pressure on Islamabad to step up its efforts against Taliban and al Qaeda militants launching attacks on Western forces in Afghanistan from Pakistani sanctuaries.