Revelations this year about torture by the CIA and electronic spying by the NSA have hurt the agencies' public image, casting them as aggressive or nosy rather than _ as they tend to see themselves _ quiet patriots forced to work in obscurity to protect the nation.
Officials say falling morale has affected the agencies' ability to hold on to employees _ often highly skilled analysts and technicians who could earn much more money in the private sector. Attrition at the National Security Agency has increased by half in the past year.
And now they face a new challenge: working for a boss who has shown little interest in their work.
As a candidate, Donald Trump dismissed the intelligence community's conclusion that Russia had hacked the Democratic National Committee's emails. As president-elect, he has said he doesn't need the daily intelligence briefing ordinarily given to presidents.
And when the CIA concluded that Russian hacks were aimed specifically at getting Trump elected, his aides attacked the messenger.
"These are the same people that said Saddam Hussein had weapons of mass destruction," his transition team said.
Rep. C.A. Dutch Ruppersberger, D-Md., whose district includes the NSA headquarters at Fort Meade and many of its employees, said the president-elect needs to take time to better understand what the intelligence agencies o, and how they can help him govern.
Ruppersberger, who was a member of the House Intelligence Committee for 12 years, said he urged Rep. Mike Pompeo, the Kansas Republican Trump has chosen to lead the CIA, to intercede.
"No president of the United States can be an effective commander in chief unless he relies on his intelligence agencies," Ruppersberger said. "He's going to need these agencies just like he's going to need the military."
Trump said on Fox News last week that the stories about Russia were being spread by his Democratic opponents, and that the intelligence community didn't know who was behind the hacks.
He said he didn't need regular intelligence briefings because "you know, I'm, like, a smart person."
Mark Stout, director of the intelligence program at the Johns Hopkins University, said other presidents have entered office skeptical about the intelligence community.
Richard Nixon was suspicious of the CIA for what he saw as its tendency to hire from elite schools. Jimmy Carter was concerned by the agency's covert action programs.
But Trump's comments, he said, are unprecedented.
"This is a serious profession that only a few people are able to do," said Stout, a former analyst for the State Department and the CIA. "This takes real work and real expertise. And to have someone dismiss it out of hand as being done for partisan reasons or being done by a group of incompetents has got to rankle."
The NSA has long focused on retaining its highly skilled employees. Part of the agency's pitch is its mission: It offers them a unique opportunity to protect their nation.
But now the agency is in the midst of a major reorganization that has proved unpopular in some quarters.
The NSA was once so secret that government officials denied its existence _ the joke was the acronym stood for No Such Agency.
But it has been shaken by the unusually public revelations by Edward Snowden of its worldwide spying programs.
Snowden, a former NSA contractor from Maryland, revealed programs that collected emails and other electronic communications involving suspected terrorists, and gathered data on huge numbers of telephone calls that could have involved, potentially, anyone.
Keith Alexander, the former Army general who led the NSA until 2014, said the agency and its work have been misunderstood, which has damaged employee morale.
Agency officials have taken pains to explain that while the NSA gathered "telephony metadata" _ phone numbers, and the times and lengths of the calls _ the agency did not record or listen to the conversations themselves.
The email program did capture Americans' communications in some cases.
Adm. Michael Rogers, the current NSA director, has said the increased monitoring of employees since Snowden stole secrets and fled the country has also frustrated the staff.
Meanwhile, stories like one Alexander shared at the University of Maryland this month, about hundreds of agency employees helping to stop a bomb attack in Afghanistan, often don't reach the public.
An internal NSA document obtained by The Baltimore Sun shows the agency had been working to retain employees for years before Snowden. The agency began to notice an increase in attrition in 2009.
The NSA's current attrition rate is just under 6 percent, a spokesman said, up from less than 4 percent in January. From October 2015 to March 2016, 117 technical workers resigned, according to the document.
The agency asked them their reasons for leaving; six in 10 who responded said the cost of living in Maryland led to their decision.
One employee cited different parking arrangements after getting a new assignment.
"Changing positions ... added another 10 to 15 minutes to each end of the day for parking," the employee wrote.
Others said better pay would have persuaded them to stay. But many have technical skills that can be more lucrative in the private sector.
"NSA is creating the talent other organizations need," the document says.
The document predates the implementation of NSA21, the reorganization effort.
Intended to allow the agency to more effectively fight hackers and gather information online, NSA21 ended the traditional distinction between defensive and offensive teams. But it also split some units apart _ the elite Tailored Access Operations hacking team, for example, has been shaken up, two people familiar with the changes said on the condition of anonymity.
Different functions of the unit are being split among new divisions created by the NSA21 program, according to a former cyber operative who retains close ties to the agency, and that means managers have less autonomy to make independent decisions, and have to fight harder for resources.
"Leadership doesn't like it at all," said the former operative, who spoke on the condition of anonymity.
Ruppersberger said that he was monitoring the reorganization and that some employees were unhappy.
"No one likes change or reorganization," he said.
Kathy Hutson, the NSA's human resources chief, said the agency continues to attract the kinds of workers it needs to carry out its mission.
Alexander, the former director, said a combination of poor morale inside the agency and attractive opportunities outside could push employees away.
"People with cyber experience in some of these large companies make up to seven figures," he said. "That's five times what the chairman of the Joint Chiefs makes."
