WASHINGTON — The director of the Defense Intelligence Agency, Lt. Gen. Michael T. Flynn of the Army, and his civilian deputy, David R. Shedd, will retire by early fall, the agency said in an email to its employees on Wednesday.
The two men are stepping down at a time when the Defense Intelligence Agency is shifting its priorities from providing intelligence to troops in Iraq and Afghanistan to working more closely with the C.I.A. to gather and distribute information on global issues like the proliferation of weapons and rising powers like China.
In a statement, the Pentagon spokesman, Rear Adm. John Kirby, said that Defense SecretaryChuck Hagel “appreciates the service of these two dedicated and professional leaders,” and that the retirements had been planned “for some time.”
But two senior American officials said tensions had flared between General Flynn and some of his Pentagon colleagues who balked at changes he wanted to make, including cuts to what he viewed as outdated intelligence programs in favor of devoting shrinking resources to newer threats, including in the digital realm.
General Flynn, whose 33-year Army career has included combat tours in Iraq and Afghanistan, has led the agency’s 16,500 employees since July 2012. He served as the top intelligence officer for the Joint Chiefs of Staff before he went to Kabul to oversee a revamping of the mission in Afghanistan. At the Defense Intelligence Agency, he pioneered new intelligence techniques to understand terrorist and insurgent networks, and to track and attack their leadership. But his hard-charging style and innovations alienated some officials.
“Anytime you have a leader with Mike Flynn’s incredible energy and drive, you’re bound to cause a rub every now and then, both inside your organization and within your change of command,” said one of the American officials, who spoke on the condition of anonymity to discuss personnel matters. “He’s a guy who can shake things up.”
The other senior American official said, “It was a mutual agreement that there needed to be a change in leadership.”
Mr. Shedd, a career intelligence officer, has been the deputy since August 2010. No replacements were named, but a Pentagon official said that the administration intended to send nominations to the Senate by the Memorial Day recess next month in order to gain approval by the fall.
The Defense Intelligence Agency’s main role is to defend American forces, but General Flynn found in his tenure that often meant defending the military’s computer networks. During his time, an Iranian attack on the Navy’s systems led to an effort to understand how a middling power managed to wreak havoc, though in a system that was not central to controlling the Navy’s assets around the world.
“Our defense networks are constantly being probed, attacked, exploited,” the general said at a session at Harvard’s Kennedy School of Government in February, describing the difficulty the military faces determining “the attribution of who is really behind it.” But he said he was less concerned about how the United States protects its defense networks than how it fails to protect civilian networks. “I am worried about power plants, financial institutions health care systems — that is an area where there are a lot of weaknesses.”
Mr. Shedd rose in the ranks of the C.I.A. in a range of critical roles and was viewed as one of the country’s top analytic minds, and a potential director for the spy agency. He moved to the White House at the height of the wars in Iraq and Afghanistan, in a role as the National Security Council’s main conduit to the nation’s intelligence agencies.
He was a central player in setting up the Office of the Director of National Intelligence, but his role there created major tensions with the C.I.A., where there was considerable resistance to the creation of the office, which was viewed as diminishing the influence of the C.I.A. and its director.
Partly as a result, Mr. Shedd never returned to the C.I.A.; instead, he worked in a crucial role at the National Intelligence Office before moving to the Defense Intelligence Agency. He focused heavily on the uprising in Syria.
Last July, he warned that the Syrian conflict could last “many, many months to multiple years,” and described a situation that would most likely worsen regardless of whether the Syrian leader, President Bashar al-Assad, fell.
Mr. Shedd suggested that in addition to strengthening the more secular groups of the fractious Syrian opposition, the West would have to directly confront more radical Islamist elements.
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