Lt. Gen. Michael Flynn, the head of the Defense Intelligence Agency, has announced that he is stepping down later this year. Flynn has run the Defense Department's intelligence agency for almost two years and was slated to be in the post for an additional year. He will continue to head the agency until the early fall.

Known as an innovator in intelligence collection and analysis, Flynn instituted changes at the DIA intended to transform the agency's methods and which may have come into conflict with the rest of the intelligence community.

In a joint message to the DIA workforce released Wednesday Flynn and his deputy, David Shedd, announced that both would retire from their DIA post. A DIA spokesperson said Shedd's retirement had been long expected.

Though his changes at DIA have reportedly led to clashes with other senior intelligence officials, a U.S. official said Flynn was stepping down for personal reasons following a 33-year military career.

In their message Flynn and Shedd said, "As we look back on our nearly 70 combined years of service to DIA, our military, the Intelligence Community (IC), and to our nation, we are proud of the legacy of sustained superb performance of the thousands of men and women we have served alongside throughout these many years. It has been our distinct honor to serve with you and so many others in defense of our nation."

Flynn was a strong advocate for expanding the role of the DIA's human intelligence gathering arm known as the Defense Clandestine Service, a move that led to conflict with other members of the intelligence community and on Capitol Hill.

At an intelligence symposium in October, 2012 Flynn spoke of his plans to integrate the Defense Clandestine Service more into the intelligence community. "I'm going to use this to integrate the entire agency," Flynn said. "This is not a marginal adjustment for DIA. This is a major adjustment for national security."

In their statement Flynn and Shedd said, "Today and tomorrow DIA is clearly postured to achieve even greater heights due to the establishment of our fully integrated intelligence centers, enhancements to all-source analysis and building the Defense Clandestine Service."

DIA spokesperson Susan Strednansky said that during their tenures Flynn and 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."

She said that transformation "has enabled the agency to nimbly respond to recent crises without having to create special task forces or move people."

Prior to arriving at the DIA, Flynn developed a reputation as an innovator in tracking insurgent networks in Iraq and Afghanistan working alongside Gen. Stanley McChrystal at the military's secretive Joint Special Operations Command. They created fusion cells that integrated traditional intelligence collection with new intelligence gleaned from Special Operations raids that led to further raids and targets.