It’s a Tough Time to Be the Intelligence Chief

Although his confirmation as the nation’s first intelligence director is likely weeks away, John D. Negroponte’s inbox is already full of thorny problems -- among them interagency squabbles and ethical questions over the handling of prisoners -- that he will be expected to resolve.

If confirmed by the Senate, Negroponte would be taking charge of the U.S. intelligence community at a time when the aggressive methods it has embraced since the Sept. 11 terrorist attacks are under growing scrutiny. As a result, the community’s flagship agency -- the CIA -- is growing increasingly uncomfortable in its role as jailer and interrogator of high-ranking terrorism suspects.

Negroponte also would be stepping into a raging debate over how billions of dollars in spy agency budgets are being spent.

In particular, he may be thrust into the role of refereeing a dispute between powerful lawmakers and the Pentagon over a costly spy satellite program that influential senators would like to kill.

Negroponte, currently U.S. ambassador to Iraq, is likely as well to need all of his diplomatic skills to handle emerging boundary disputes between the CIA, the FBI and the Pentagon as the latter two agencies expand their intelligence collection operations.

These are just some of the nettlesome issues he would confront in the moments when he was not overwhelmed by his principal responsibility: overseeing the first major restructuring of the U.S. intelligence community in more than 50 years.

Negroponte is a “savvy, experienced diplomat who understands the real, harsh world in which intelligence operates,” said James L. Pavitt, who retired last year as head of the CIA’s clandestine service. But he added that Negroponte and Lt. Gen. Michael V. Hayden, who was nominated as deputy intelligence chief, “have got one hell of a job ahead of them.”

Negroponte and Hayden, the head of the National Security Agency, were nominated Thursday by President Bush to fill new intelligence posts created last year by Congress to provide American spy agencies with central leadership. The aim is to end the confusion and lack of communication that contributed to failures surrounding the Sept. 11 attacks.

In interviews Friday, current and former intelligence officials applauded Bush’s choices for the jobs, with one U.S. intelligence official saying the reaction he had seen among employees in the CIA was “uniformly positive.” Several officials expressed relief that the nominations had gone to a diplomat and a longtime intelligence professional, after months of rumors that the positions might be awarded to political operatives.

Negroponte is “a real player, a solid guy who understands what intelligence can and can’t do,” said a former senior CIA official who worked with Pavitt and left the agency last year. “If they had picked a political partisan, a known protege of Vice President Cheney or [Defense Secretary Donald H.] Rumsfeld, it would have been chilling.”

Although some question whether Negroponte would have the authority needed to succeed, they said he was likely to get support from the CIA and the other 14 agencies that make up the U.S. intelligence community. Beyond the challenge of managing the restructuring of those agencies, the officials pointed to a number of looming issues that could require Negroponte’s attention.

Among them is the growing controversy surrounding the CIA’s role in detaining and interrogating terrorism suspects at secret locations around the world, as well as its practice of turning some prisoners over to other countries, including Egypt, that have been accused of engaging in torture.

CIA officials reacted with dismay last year as the Justice Department backpedaled from legal opinions that seemed to endorse the agency’s use of such methods as water-boarding, in which prisoners are made to believe they are drowning.

Democrats on the Senate Intelligence Committee are pushing for a thorough investigation of the CIA’s detention and interrogation practices. Sen. John D. Rockefeller IV (D-W.Va.), the ranking Democrat on the panel, said in an interview Friday that he expected to reach an agreement on an investigation with the Republican chairman of the panel, Sen. Pat Roberts of Kansas, in the coming weeks.

Rockefeller said he believed Negroponte should conduct his own review of CIA detention and interrogation policies.

“That’s one of the reasons I’m very glad he’s there,” Rockefeller said.

Amid the mounting scrutiny, CIA officials are pushing for a reduced role in detention operations, a development first reported last week in the New York Times.

“There’s some discussion, and it’s interagency, about what you do with these people long term,” said a U.S. intelligence official, referring to Khalid Shaikh Mohammed and other alleged senior Al Qaeda operatives in custody at undisclosed CIA facilities overseas.

“You’ve got to wonder: What do you do with these people once their intelligence value has been fully exploited,” the official said. “The CIA is an intelligence collection and analysis organization. This isn’t the bureau of prisons.”

The CIA and its contractors have come under criticism in reports and investigations into detainee abuses in Iraq and Afghanistan. The agency has been accused of harboring dozens of undocumented “ghost” detainees and sometimes brutally interrogating prisoners, leading to at least one case of a detainee’s death after a beating by a CIA contractor.

One of the most sensitive and risky aspects of Negroponte’s job, intelligence officials said, would be deciding where the United States should concentrate its already stretched intelligence resources, from spy satellites in the sky to paramilitary operatives on the ground.

CIA Director Porter J. Goss acknowledged the challenge in congressional testimony last week, saying, “We need to make some tough decisions about which haystacks deserve to be scrutinized for the needles that can hurt us most.”

Before taking the CIA job, Goss had criticized the agency for focusing too much on terrorism, which still rankles officials who were in senior positions at the agency at the time. Pavitt said Negroponte would have to “stay the course on terrorism and stay the course on Iraq,” two areas that were “sucking up huge amounts of scarce resources.”

“When you have someone saying we’ve over-devoted resources to terrorism, over-devoted resources to Iraq, [Negroponte] is going to have to say, ‘What does that mean?’ ” Pavitt said. “ ‘Do you really think we’re not spending enough time on Haiti?’ ”

Another brewing conflict is likely to test Negroponte’s authority over intelligence agency budgets as well as his willingness to confront the Pentagon. At issue is a top-secret spy satellite program that has come under attack from influential lawmakers.

Known by the code name “Misty,” the program is aimed at developing satellites that can orbit undetected. But its cost has mushroomed, from $5 billion to $9.5 billion. Opponents argue that spy planes can do the job, and that the money would be better spent in areas more critical to defending against terrorism, including the hiring of more human spies.

The debate surfaced publicly last year when Sen. Rockefeller protested on the Senate floor what he described as a “totally unjustified and very, very wasteful” program. He did not describe its nature, but other officials said he was referring to Misty.

The Senate Intelligence Committee has tried to kill the program, only to be outmaneuvered by the Pentagon in congressional funding battles.

One of Negroponte’s main functions, as described by Bush on Thursday, is controlling spy budgets. If he reaches the same conclusion as the Senate committee and is prepared to face down Rumsfeld, he could terminate the program.

“Don’t think I haven’t thought about that,” Rockefeller said. “There are various ways to attack that program, to abolish that program. That’s going to have to be handled before it gets too far down the line.”