The plane took off amid a hail of bullets, according to the Colombian air force and the civil aviation agency.
The aircraft, a Cessna 210 with a false Guatemalan registration, was apparently used for drug trafficking and, the air force said, had been impounded after entering Colombia illegally.
The small plane came from Honduras and "was detected, intercepted and forced to land" on Dec 11, 2011, and was being held at Los Cedros airport in Uraba, the air force said.
The robbery took place Sunday night and was carried out by a group of armed men who seized it in the hangar where it was being guarded, taxied it onto the runway and took off amid shots by police trying to stop it.
The air force said that its control systems "tracked the aircraft until it crossed into Panamanian air space and informed the Central American countries with which an has an interdiction agreement".
"As yet we have no information as to the whereabouts of the aircraft," the air force said, adding that it will "remain alert to any request and will support Central American authorities in their search for the aircraft".