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.

Gimigliano, the CIA spokesman, declined to comment on the agency’s financial ties to Afghan officials. “This agency plays an essential role in promoting American goals in Afghanistan, including security and stability,” he said. “Speculation about who may help us achieve that is both dangerous and counterproductive.”

The agency’s approach has drawn criticism from others in the U.S. government, who accuse the CIA of contributing to an atmosphere in which Afghans are conditioned to extend their hands for secret payments in almost every transaction.

“They’ll pay whoever they think can help them,” the U.S. official said. “That has been the CIA attitude since 2001.”

A second U.S. official defended the agency’s activities and alluded to a simmering conflict within the U.S. government over the scope of American objectives in Afghanistan, and the means required to achieve those goals.

“No one is going to create Plato’s Republic over there in one year, two years, or 10,” the official said. “If the United States decides to deal only with the saints in Afghanistan, it’s in for both loneliness and failure. That’s the risk, and not everyone in our government sees it.”

U.S. and Afghan officials said the CIA is not the only foreign entity using secret payments to Afghan officials to influence events in the country.

A prominent Afghan with knowledge of the inner workings of the palace said it operates a fund that rewards political allies with money that flows in from the Iranian government and foreign intelligence services as well as prominent Afghan companies eager to curry favor with Karzai. The source said the fund distributes $10 million to $50 million a year.

A U.S. official said Turkey and Saudi Arabia are among the other countries funneling money into Afghanistan.

Salehi, the target of the corruption probe, is accused of taking a bribe in return for his help in blocking an investigation of New Ansari, a money transfer business that has helped elite Afghans ship large sums of cash to overseas accounts. U.S. officials worry that the stream includes diverted foreign aid.

But authorities said the Salehi investigation is also focused on his involvement in administering the palace fund – doling out cash and vehicles to Karzai supporters – as well as his role in negotiations with the Taliban.

Salehi’s job put him at the center of some of the most sensitive assignments for the Afghan government. Another national security official, Ibrahim Spinzada, has orchestrated the government’s talks with the Taliban and traveled with Salehi to Dubai, Saudi Arabia and Russia.

The payments from the palace are “part of the politics here,” said a second senior Afghan official. Some people receive “a special salary. It is part of intelligence activities.”

Rangin Dadfar Spanta, Afghanistan’s national security adviser and Salehi’s boss, said in an interview that he had spoken with Salehi on Thursday and that Salehi denied working with the CIA. “I don’t think that Salehi is a spy,” Spanta said, adding that Salehi was “shocked and he absolutely rejected it.”

U.S. officials did not dispute that Salehi was on the CIA payroll, which was first reported by The New York Times. But officials sought to draw a distinction between agency payments and corruption probes.

“The United States government had nothing to do with the activities for which this individual is being investigated,” the second U.S. official said. “It’s not news that we sometimes pay people overseas who help the United States do what it needs to get done. . . . Nor should it be surprising, in a place like Afghanistan, that some influential figures can be both helpful and – on their own, separate and apart – corrupt to some degree.”

The flow of CIA money into the region dates to the agency’s support for mujaheddin fighters who ousted Soviet forces three decades ago.

The spigot was tightened during the 1990s but reopened after the terrorist attacks of Sept. 11, 2001. Much of the money went to support warlords whose militias helped to overthrow the Taliban regime, which had provided sanctuary for Osama bin Laden and al-Qaeda training camps. Salehi had served as an interpreter for one of the most prominent of those warlords, Abdurrashid Dostum, an ethnic Uzbek whose forces played a critical role in the campaign against the Taliban.

The CIA bankrolled Afghanistan’s intelligence service, and its financial ties to government officials has proliferated in recent years.

“There are probably not too many officials we haven’t met and contacted and paid,” a former CIA official said.

The CIA has a long-standing relationship – though not a financial one – with Karzai himself. The agency’s station chief in Kabul traveled with Karzai during the war against the Taliban, at one point shielding him from the blast of a misdirected bomb. The station chief has since served two tours in the Afghan capital at Karzai’s behest.

The payments are long-standing in many cases and designed to help the agency maintain a deep roster of allies and sources within the presidential palace. They have continued despite concerns that the agency is backing corrupt officials and undermining efforts to wean Afghans’ dependence on secret sources of income and graft.

“Half the palace is on the payroll,” said a U.S. official, who added that some officials function as agency informants but that others collect stipends under more informal arrangements meant to ensure their accessibility to the CIA.

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.

“Karzai is blind to about 80 percent of what’s going on below him,” he said.

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 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 to humiliate the Afghan leader while ignoring more pressing priorities.

In the latest sign of his vexation, Karzai said Thursday that President Barack Obama’s timeline for withdrawing U.S. troops “has given courage to the enemies of Afghanistan,” and complained the United States wasn’t doing enough to force Pakistan to stop supporting the Taliban.

The CIA has maintained relationships with Afghan government officials for years. But the disclosure that perhaps dozens of 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.

A CIA spokesman declined to comment on the agency’s financial ties to Afghan officials. “This agency plays an essential role in promoting American goals in Afghanistan, including security and stability,” said the spokesman, Paul Gimigliano. “Speculation about who may help us achieve that is both dangerous and counterproductive.”

The agency’s approach has drawn criticism from others in the U.S. government, who accuse the CIA of contributing to an atmosphere in which Afghans are conditioned to extend their hands for secret payments in almost every transaction.

“They’ll pay whoever they think can help them,” the U.S. official said. “That has been the CIA attitude since 2001.”

A second U.S. official defended the agency’s activities and alluded to a simmering conflict within the U.S. government over the scope of American objectives in Afghanistan and the means required to achieve them.

“No one is going to create Plato’s ‘Republic’ over there in one year, two years, or 10,” the official said. “If the United States decides to deal only with the saints in Afghanistan, it’s in for both loneliness and failure. That’s the risk, and not everyone in our government sees it.”

U.S. and Afghan officials said the CIA is not the only foreign entity using secret payments to influence events in the country.

A prominent Afghan with knowledge of the inner workings of the palace said it operates a slush fund that rewards political allies with money that flows in from the Iranian government and foreign intelligence services as well as prominent Afghan companies eager to curry favor with Karzai. The source said the fund distributes from $10 million to $50 million a year.

A U.S. official said Turkey and Saudi Arabia are among the other countries funneling money into Afghanistan.

U.S. officials did not dispute that Salehi was on the CIA payroll. But officials sought to draw a distinction between agency payments and corruption probes.

“The United States government had nothing to do with the activities for which this individual is being investigated,” the second U.S. official said. “It’s not news that we sometimes pay people overseas who help the United States do what it needs to get done … . Nor should it be surprising, in a place like Afghanistan, that some influential figures can be both helpful and – on their own, separate and apart – corrupt to some degree.”