Santos ordered Defense Minister Juan Carlos Pinzon to travel to the isolated Choco department town of Quibdo to lead the investigation into yesterday's presumed "abduction" of Brigadier General Ruben Alzate.
"We demand that his captors (all signs point to the FARC) set him free as soon as possible, and safe and sound," Santos said on Twitter.
The general lost contact with ground forces in Quibdo, in the southwest, where the FARC is active.
The FARC is currently locked in dialogue with Colombian government negotiators attempting to broker a peace deal to end the five-decade-long conflict.