Supposedly, that is exactly how genjutsu work. You "pump" chakra into their brain/nervous system and take control of it by swamping their chakra out. If the victim has enough chakra, he can mold a bunch and override the override. In fact, that is why Killer Bee was immune to Sasuke's Sharingan. He explained that a jinchuuriki who can control his bijuu is pretty much immune to genjutsu, because they can call on a huge amount of chakra to override the genjutsu's effects.
Naruto supposedly sucks at genjutsu (and we've never seen him train for it), but he has a couple of techniques that let him manipulate chakra outside of his body, and he really wouldn't need to control a guy's brain -- he'd just have to pump in natural energy.
Also, we can possibly compare this idea to Gedo Mazo's "Instant Kill Ghost" attack from when Pein was fighting Salamander Hanso. Weird "ghost" tentacles came out of the statue and instantly killed anyone they touched. That's unlike anything else we've seen, except for genjutsu (in the way I described above). Maybe that was a "chakra pumping" move that messed up people's nervous systems.