A draft report by UN experts sent to Panama after the seizure of the ship in July confirmed a breach of sanctions, the ministry of public security said.
Two North Korean diplomats are in Panama to assist the ship’s 35 crew.
Cuba said it shipped the arms to North Korea for repair. It did not say why they were hidden under tonnes of sugar.
A source in the public security ministry said authorities had been given a first draft of the report compiled by UN sanctions panel experts, the AFP news agency reports.
The ship, the Chong Chon Gang, was seized on suspicion it was carrying drugs.
The vessel had been navigating the Panama Canal.
Officials found 25 containers of military hardware, including two Soviet-era MiG-21 fighter aircraft, air defense systems, missiles and command and control vehicles.
The statement from the Panamanian public security ministry was released after the North Korean diplomats – from the country’s mission in Havana – visited the crew members at a former military base.
They are being detained on suspicion of arms trafficking; an offence which carries a 12-year prison sentence.
The UN inspectors completed their work two weeks ago but are yet to present their official findings publicly.
The 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.
The ship 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.
It was stopped near Manzanillo on the Atlantic side of the canal on July 15.
Under UN sanctions, North Korea is banned from weapons exports and the import of all but small arms.
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