Director of National Intelligence James Clapper, left with CIA Director John Brennan, is concerned that federal budget cuts will hurt intelligence operations. Today’s cutbacks, known as sequestration, will harm the nation in ways that might not be known until it is too late, he said. (Alex Wong/Getty Images)

James Clapper has seen a lot during a government career that began when President Obama was in diapers.

Not all of it was pretty.

Clapper spent a brief period in the Marine Reserve before becoming a second lieutenant in the Air Force in 1963, two years after Obama was born. He flew combat support missions over Laos and Cambodia during the Vietnam War. He worked his way up to lieutenant general and, in 1991, was made director of the Defense Intelligence Agency.

What worries him now, as director of national intelligence, is a rerun of federal budget cuts that he said hurt intelligence operations in the 1990s. Today’s cutbacks, known as sequestration, will harm the nation in ways that might not be known until it is too late, he said. Employee furloughs are under consideration, though none has been announced.

“We’re cutting real capability and accepting greater risk,” Clapper told reporters in his office Friday. “For intelligence, this is not quite like shorter hours for public parks or longer lines at the airports. For intelligence, it’s insidious.

“The capability we cut out today, you won’t know about that, you won’t notice it,” he said. “The public won’t notice it. You’ll notice it only when we have a failure.”

His Office of Director of National Intelligence (ODNI) is charged with fostering integration among 16 intelligence agencies. Clapper provided no details of how cuts could compromise intelligence capabilities. He did, however, provide a history lesson.

“I’ve seen this movie before,” he said, referring to cuts in the 1990s. “We closed CIA stations overseas. We cut human intelligence, we let our overhead reconnaissance architecture atrophy. We neglected the basics like power, space and cooling . . . and most painfully we allowed the workforce to be distorted.”

Then came the Sept. 11, 2001, terrorist attacks. Intelligence budgets grew. But now, he said, “we’re in another cut cycle.”

Clapper stressed the importance of maintaining the workforce, even as he acknowledged the possibility of making employees take unpaid leave days.

“This is . . . a big deal to me,” Clapper said. “It is a uniform conviction across the leadership of the intelligence community that the most important resource we have is our people. So I’m going to try to do all I can — all of us are — to protect our people. If we have to furlough, then minimize the damage and the impact of doing that. All that hasn’t been worked out.”

Just the specter of furloughs “has huge morale impacts,” he said. “I will do all I can to avoid that.”

Rep. Mike Rogers (R-Mich.), chairman of the House Permanent Select Committee on Intelligence, said that he shares Clapper’s concern about the sequester’s operational affects and risks to intelligence. “However, the enactment last month of the full year FY 13 [fiscal year 2013] defense appropriations act will help avoid the worst national security impacts of the sequester.”

Among the areas Clapper identified that could be hurt by budget cuts are recruiting, improving the security clearance process and increasing personnel diversity.

“That’s one of the things I’m very sensitive about, the impact of sequestration on diversity in the community,” he said. “You can argue that not only should we look like America, we should look like the world in the intelligence community, which we don’t.”

A look at the ODNI leadership Web page provides a stark example of that. Of 15 photos, there is only one person of color, a man of Indian descent. A list of 25 top agency officials includes five racial minorities and five women, according to an agency spokesman. ODNI statistics indicate intelligence agencies were about 77 percent white and 66 percent male during fiscal year 2012.

“All of the arrows are going in the right direction,” Patricia Taylor, the intelligence community’s chief of equal opportunity and diversity, said as she listed various programs aimed at encouraging students to consider intelligence work. The agencies are “making a lot of progress in the upper pay grades and senior positions,” she said.

Security clearances now take less time to process, but Clapper fears that could be hurt by budget cuts. Also, while updating security clearances every five years is the current practice, “that’s one thing that people are making some decisions about, again taking a risk not to do that.”

Like other agencies, recruiting by the intelligence community, which ranks high in employee surveys, could be hurt by the budget cuts.

When recruiters court a bright college prospect, they can stress the “very important, crucial work” of intelligence employees, Clapper said. But he added that recruiters also will have to tell prospects to “bear in mind your pay is going to be capped, and you’re subject to whimsical furloughs.”

“How attractive do you think that’s going to be over time?” he asked.

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