Lt. Gen. Michael T. Flynn abruptly announced his retirement Wednesday as head of the Defense Intelligence Agency, after what current and former officials said were clashes with his boss and other opponents inside the Pentagon spy service.
Flynn's deputy, David R. Shedd, is also retiring, according to a statement from the agency.
The agency collects and analyzes foreign intelligence to support the U.S. military. The better known CIA is a civilian agency that reports to the president.
Flynn, who took over the agency in July 2012, clashed repeatedly with his superior, the Pentagon's undersecretary for intelligence, Michael Vickers, a senior Defense official said.
"He was trying to take DIA in a direction the rest of the department didn't want to go," the official said.
A former agency official and Flynn supporter said Flynn was undermined by an "old guard" at the agency who resisted changes he wanted to make. He sought to cut what he viewed as outdated intelligence programs in favor of allocating resources to newer threats, including cyber.
"Gen. Flynn wanted to take advantage of the budget pressures and the demand for a more adaptive agency to bring change and find efficiencies," the former official said. "DIA is a bloated bureaucracy with overstaffed analytical elements still focusing on requirements that have been overtaken by applications in technology."
[Updated, 4:11 p.m. PDT April 30: Asked to respond, DIA said in a statement:
"During their tenure, LTG Flynn and Mr. Shedd led an agency transformation that has brought much needed integration to the agency's intelligence operations, efficiency to business processes and has shaped and developed the workforce – applying lessons learned during more than a decade of war.
"That transformation has enabled the agency to nimbly respond to recent crises without having to create special task forces or move people."]
No immediate successor was announced. One potential candidate mentioned in the Pentagon is Lt. Gen. Mary A. Legere, the Army's deputy chief of staff for intelligence.
Flynn served as a top intelligence advisor to Gen. Stanley McChrystal in Iraq and Afghanistan.
In 2010, he wrote a scathing report titled "Fixing Intel" arguing that military intelligence was largely irrelevant to the counterinsurgency campaign in Afghanistan.