http://www.nytimes.com/2010/12/30/world/asia/30disappear.html WASHINGTON â€” The Obama administration is expressing alarm over reports that thousands of political separatists and captured Taliban insurgents have disappeared into the hands of Pakistanâ€™s police and security forces, and that some may have been tortured or killed. The issue came up in a State Department report to Congress last month that urged Pakistan to address this and other human rights abuses. It threatens to become the latest source of friction in the often tense relationship between the wartime allies. The concern is over a steady stream of accounts from human rights groups that Pakistanâ€™s security services have rounded up thousands of people over the past decade, mainly in Baluchistan, a vast and restive province far from the fight with the Taliban, and are holding them incommunicado without charges. Some American officials think that the Pakistanis have used the pretext of war to imprison members of the Baluch nationalist opposition that has fought for generations to separate from Pakistan. Some of the so-called disappeared are guerrillas; others are civilians. â€œHundreds of cases are pending in the courts and remain unresolved,â€ said the Congressionally mandated report that the State Department sent to Capitol Hill on Nov. 23. A Congressional official provided a copy of the eight-page, unclassified document to The New York Times. Separately, the report also described concerns that the Pakistani military had killed unarmed members of the Taliban, rather than put them on trial. Two months ago, the United States took the unusual step of refusing to train or equip about a half-dozen Pakistani Army units that are believed to have killed unarmed prisoners and civilians during recent offensives against the Taliban. The most recent State Department report contains some of the administrationâ€™s most pointed language about accusations of such so-called extrajudicial killings. â€œThe Pakistani government has made limited progress in advancing human rights and continues to face human rights challenges,â€ the State Department report concluded. â€œThere continue to be gross violations of human rights by Pakistani security forces.â€ The Obama administration has largely sought to confront Pakistan in private with evidence of human rights abuses by its intelligence and security forces, fearing that a public scolding could imperil the countryâ€™s cooperation in combating Al Qaeda, the Taliban and other extremist groups. After the Sept. 11 attacks, the administration of President George W. Bush urged Pakistan to capture militants and Islamic extremists linked to the Taliban and Al Qaeda. Since then, human rights groups have said that Pakistanâ€™s security forces used that campaign as a cover to round up hundreds, if not thousands, of political activists and guerrilla fighters in Baluchistan and hold them in secret detention. Precise numbers of disappearances are difficult to pin down, human rights advocates say, partly because family members fear that reporting missing relatives could endanger the relatives or even themselves. â€œIt is very difficult to put numbers on disappearances as they are accompanied by intimidation of the next of kin of the disappeared,â€ said Ali Dayan Hasan, a senior researcher for Human Rights Watch in Lahore, Pakistan. â€œPeople are unable to speak publicly. But we can safely say that disappearances are the order of the day across Pakistan, particularly in relation with counterterrorism.â€ In Islamabad on Wednesday, the interior minister, Rehman Malik, addressed the security issue in Baluchistan without mentioning the disappearances. â€œWe are trying to ensure law and order in Baluchistan,â€ he told lawmakers in the National Assembly. â€œI will assure that we will do everything to improve the situation.â€ In August 2009, he acknowledged that 1,291 people were missing in the country. Husain Haqqani, Pakistanâ€™s ambassador to Washington, said in an e-mail on Wednesday that â€œthe courts and the government are investigating cases of disappearances with a view to establishing the whereabouts of the disappeared persons and the circumstances under which the alleged disappearances took place.â€ Under pressure from Pakistanâ€™s Supreme Court, which has held hearings on petitions filed by family members of missing Baluch men, as well as public rallies in supported of the disappeared, the government of President Asif Ali Zardari has been forced to respond to the outcry. A judicial commission established to investigate the disappearances is scheduled to present its report to the Supreme Court on Friday. Pakistani intelligence officials say that human rights groups have exaggerated the number of people held incommunicado. The officials seemed to justify the extrajudicial detentions by citing the countryâ€™s weak judicial system and often poor police investigations that they say have led to dozens of terrorism suspectsâ€™ being acquitted by local courts. American officials have dismissed these claims for years. â€œ â€˜Disappearedâ€™ Pakistanis â€” innocent and guilty alike â€” have fallen into a legal black hole,â€ the United States Embassy in Islamabad said in a cable, dated Feb. 8, 2007, that was obtained by WikiLeaks and made available to some news organizations, including The New York Times. American officials are expanding programs to build up the judicial system in Pakistan. Officials also offer human-rights training to police officers and finance programs to reduce the backlogs of court cases that prevent family members of those who disappear from seeking relief through the Pakistani judicial system. â€œThis issue has been a persistent challenge for Pakistan,â€ said a senior American official who deals with South Asia and who spoke on condition of anonymity because of the delicacy of the matter. â€œWeâ€™re trying to help Pakistan build democratic institutions so they can be a more effective partner.â€ But American officials concede that the programs may take years to produce enduring results. The State Departmentâ€™s most recent report on human rights in Pakistan, issued in March, said that during 2009 â€œpolitically motivated disappearances continued, and police and security forces held prisoners incommunicado and refused to disclose their location.â€ That report, citing a Pakistani human rights group, said that in August 2009, Pakistani Frontier Corps paramilitary troops arrested two members of the Baluchistan National Party in Khuzdar, Pakistan. Two days later, the men were turned over to the police. â€œBoth men showed evidence of having been tortured,â€ the report said. â€œAuthorities reportedly forced them to make false confessions before their release.â€ Salman Masood contributed reporting from Islamabad, Pakistan.