The planes and other military items were hidden under bags of sugar and were being sent to North Korea for repairs, Cuba said.
Panama has asked the United Nations to investigate if the ship violated sanctions against North Korea prohibiting the supply of arms.
Panamanian investigators said they have found anti-aircraft radars that are capable of launching anti-aircraft weapons, in addition to the MiG-21 jets. They said evidence pointed to the MiGs having recently been flown.
"You are all here and are sensing the strong odor of fuel, to such a degree that no-one can know what danger Panama was put in," said Panama Attorney General Ana Belfon. Seven containers have been unloaded from the Chong Chon Gang so far, but officials said they expect to find more buried among the 10,000 tonnes of sugar.
Havana authorities admitted to shipping 240 tonnes of "obsolete" defensive weapons, including the jet fuselages, anti-aircraft missile complexes, nine missiles in parts and spares and 15 MiG engines.
The Chong Chon Gang left the far east of Russia on April 12 and crossed the Panama Canal in early June headed to Cuba. Satellites lost track of the ship after it left the canal and relocated it on July 11, and was stopped in Manzanillo, on the Atlantic side of Panama, on July 15.
The ship's 35-person North Korean crew has been charged with endangering Panama.