The project, previously conducted under the State Department, is now backed by the Defense Department's Office of Net Assessment. Putin's psychological profile was last updated in 2012, a Pentagon official said.
Advocates of such studies argue that it could help US officials anticipate the Russian leader's actions after he ordered troops into neighboring Ukraine, taking control of the semi-autonomous Crimean Peninsula, which has led to tensions with the West reaching levels not seen since the Cold War.
Pentagon analysts have studied about 15 foreign leaders including Russian Prime Minister Dmitry Medvedev, late Iraqi leader Saddam Hussein, North Korea's Kim Jong-Un and late Al-Qaeda leader Osama bin Laden.
Pentagon spokesman Rear Admiral John Kirby insisted "for sure" that the studies do not inform the military's policy decisions, saying Defense Secretary Chuck Hagel only learned of them following a USA Today report.
"They go right to the Office of Net Assessment, as I understand it, and they have not been used to inform any policy or program decisions here at the Department of Defense," he said.
He said about $300,000 has been spent on the studies each year since 2009.
Studying someone's body language and movements, usually using split-second video footage, can help determine behavioral habits and individual psychology, according to experts.
Pentagon researcher Brenda Connors characterized Putin's body language in 2004 as indicating he was "risk averse -- stuck in place and time" as well as being "extremely sensitive to criticism".
And in an interview in The Atlantic magazine in 2005, she said a walking problem of Putin's -- possibly because he did not crawl as a child -- "created a strong will that he survive and an impetus to balance and strengthen the body."
"He is like that ice skater who had a club foot and became an Olympic skater," Connors said. "It is really poignant to watch him on tape. This is a deep, old, profound loss that he has learned to cope with, magnificently."