The Cuban foreign ministry said the ship was carrying obsolete arms from Cuba for repair in North Korea.
The 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 continuing dispute over its nuclear programme.
However, 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 21-Bis 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 was mainly loaded with 10,000 tonnes of sugar.
The president 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.
