The suspect earlier tried to drive onto the CIA campus at McLean, Virginia, without security access and was stopped by armed guards at the gates.
During negotiations with the driver his car was pushed out of the way and it was some time after that the man got out of his car and was shot.
The suspect had claimed to have a bomb in his car, sources told CNN, but it has not been confirmed by authorities.
Officials say the man, who has not been named, was transported to an area hospital but the extent of his injuries have not been made public.
Sources told NBC News that the man has mental health issues and has tried to gain access to the CIA compound multiple times before.
“An individual involved in a security incident outside Central Intelligence Agency Headquarters in McLean, VA, emerged from his vehicle with a weapon and was engaged by law enforcement officers,” the FBI said in a statement.
“The subject was wounded and has been transported to a hospital for medical attention. The FBI takes all shooting incidents involving our agents or task force members seriously.
“The review process is thorough and objective, and is conducted as expeditiously as possible under the circumstances.”
Earlier in the day the CIA had acknowledged that they were “addressing a security situation just outside the secure perimeter of CIA Headquarters by our main gate. Our compound remains secured, and our Security Protective Officers working the incident are the only Agency personnel directly involved.”