What kind of martial arts does the CIA use?

Some cases, they want to prefer the used of close-range combat especially at unexpected inclosed spaces as long as needed. They prefer to use either Krav Maga or Judo as hand-to-hand combat arsenal. And some cases they have specialty training variety especially to use Wing Chun strikes in some organizations, If in case the matter in long-range, they don't need hand-to-hand method of combat but they often uses guns especially pistol or sidearms as their own convenient.

The CIA uses a lot of Krav Maga and Judo, but prior to Krav Maga establishing its reputation, it relied almost exclusively on Judo, and it used "dirty boxing." It also uses some Karate moves, but not many; in one infamous case, I think it was a Russian spy or some family man who discovered something during the cold war, that a CIA agent killed him with a karate chop to the throat. If the hands are conditioned enough to break boards, a direct chop the throat can indeed be fatal.

Again though, the main stay martial art of the CIA is Judo; virtually all CIA employees, even people who don't do "spy stuff," hold a black belt in it.

Jon Portos: Not wanting to criticize the above (but I am not happy with it as I actually teach advanced stealth arts): The modern Agencies use a combination of various arts as the needs of the missions of agents can be diverse and complex. No one art does all. Selected experts in different arts are engaged to teach their specialties to trainees. The Company, like other agencies in the world, also requires skills in specialist areas not found in the normal Martial Arts schools. For instance training on the use of household items as weapons, some Self Defense systems teach that.

The main weapon in such occupations though is not manipulations of one's body, but an exercising of the mind. The mind keeps you from getting into trouble, as physical skills, no matter how highly developed may be inadequate in getting you out of trouble. Also fighting is a last resort, the CIA is not Special Forces as in combat teams, although they do have similar specialists. You are not sent somewhere to fight, but to blend in and never be known. Stealth, not fighting, is the main priority of training. I might comment that hand conditioning is not recommended and is not needed in killing. You don't need to break boards. If you have to break boards then you use an axe like anyone else. You can easily kill someone without requiring hand conditioning. Also the calluses of hand conditioning cannot be hidden and therefore would be a dead give-away as to such training. And Dead here means your agent is thus discovered and dead. An expensive loss.