The payments are long-standing in many cases and designed to help the agency maintain a deep roster of allies within the presidential palace. Some aides function as CIA informants, but others collect stipends under more informal arrangements meant to ensure their accessibility, a U.S. official said. The CIA has continued the payments despite concerns that it is backing corrupt officials and undermining efforts to wean Afghans’ dependence on secret sources of income and graft. The U.S. official, speaking on condition of anonymity, said a significant number of officials in Karzai’s administration are on the payroll. Paul Gimigliano, a CIA spokesman, disputed that characterization, saying, “This anonymous source appears driven by ignorance, malice or both.” A former agency official said the payments were necessary because “the head of state is not going to tell you everything” and because Karzai often seems unaware of moves that members of his own government make. The disclosure comes as a corruption investigation into one of Karzai’s senior national security advisers – and an alleged agency informant – puts new strain on the already fraying relationship between Washington and Kabul. Top American officials including Secretary of State Hillary Rodham Clinton and Sen. John F. Kerry (D-Mass.) have expressed concern about Karzai’s efforts to rein in anti-corruption teams, as well as intervention in the case against the security adviser. The aide, Mohammad Zia Salehi, is accused of accepting a $10,000 car as a bribe in exchange for his assistance in quashing a wide-ranging corruption probe. The issue carries enormous stakes for the Obama administration. Concerns that the Afghan government is hopelessly corrupt have prompted a congressional panel to withhold billions of dollars in aid, and threaten to erode American support for the war. But Karzai supporters accuse their U.S. counterparts of exploiting the issue, and the Salehi arrest in particular, to humiliate the Afghan leader while ignoring more pressing priorities. In the latest sign of his vexation, Karzai said Thursday that President Obama’s timeline for withdrawing U.S. troops “has given courage to the enemies of Afghanistan,” and complained that the United States wasn’t doing enough to force Pakistan to stop supporting the Taliban. “We haven’t progressed in the war against terrorism,” Karzai said in a statement. The CIA has maintained relationships with Afghan government officials for years. But the disclosure that multiple members of Karzai’s government are on the CIA’s payroll underscores the complex nature of the American role in Afghanistan. Even as agency dollars flow in, U.S.-backed investigative units are targeting prominent Afghans in the government and trying to stem an exodus of more than $1 billion in cash annually from the country.