The Cuban foreign ministry said the ship was carrying obsolete Soviet-era arms from Cuba for repair in North Korea.
The North Korean ship was seized by Panama last week after “undeclared military cargo” was found hidden in a shipment of sugar.
United Nations sanctions prohibit the supply of arms to North Korea in the dispute over its nuclear programme.
A Cuban foreign ministry statement said Cuba reaffirmed its commitment to “peace, disarmament, including nuclear disarmament, and respect for international law”.
It said the vessel was carrying 240 tonnes of obsolete defensive weapons – two anti-aircraft missile complexes, nine missiles in parts and spares, two MiG-21bis fighter planes and 15 MiG engines.
The Cuban statement said they were all made in the mid-20th Century and were to be repaired and returned to Cuba.
“The agreements subscribed by Cuba in this field are supported by the need to maintain our defensive capacity in order to preserve national sovereignty,” the statement went on.
Cuba said the ship’s main cargo was 10,000 tonnes of sugar.
The vessel, called Chong Chon Gang, left Russia’s far east on April 12 and travelled across the Pacific Ocean before entering the canal at the start of June, with Cuba as its stated destination.
Panamanian officials said the ship was carrying a cargo of sheet metal on its journey through the canal.
However, the vessel disappeared from satellite tracking systems after it left the Caribbean side of the canal, resurfacing on July 11.
Experts say this may indicate that the crew switched off the system that automatically communicates details of their location.
Panamanian officials tried to communicate with the vessel, suspecting it could be carrying illegal goods initially thought to be drugs.
The crew did not respond, so the ship was boarded and the weaponry was uncovered.
North Korea and Cuba are both nominally communist states and are known to have relatively close relations.
A high-level military delegation from North Korea visited at the end of June and was received by President Raul Castro.
Cuban media said they discussed “the historical ties that unite the two nations and the common will to continue strengthening them”.
Arms trafficking expert Hugh Griffiths told the BBC the ship’s voyage could be seen in the wider context of renewed military co-operation between the two nations.
Announcing the seizure of the vessel on Tuesday, Panamanian President Ricardo Martinelli said it contained suspected “sophisticated missile equipment”.
Ricardo Martinelli posted on his Twitter account an image of a large green object inside a cargo container.
However, the Cuban statement suggests that the cargo was five decades old Soviet-era weaponry.
Panamanian officials said they had so far searched just one of the ship’s five container sections, and a full inspection would take at least a week.
The crew faces possible charges of illegal weapons smuggling in Panama.
Ricardo Martinelli said the 35-strong crew had resisted the search and the captain had tried to kill himself.
The US “commended” Panama for its actions, and said it strongly supported a full inspection of the ship.
The vessel was stopped near Manzanillo on the Atlantic side of the canal last week.
Panama released details of the find on Tuesday.
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