Outlining a dramatic sequence of events, President Ricardo Martinelli said the ship was targeted by drug enforcement officials as it approached the Panama Canal and was taken into port, but a search revealed cargo of far greater concern.
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The vessel's estimated 35-man crew also rioted when police stepped aboard, according to Martinelli, who said the suspicious goods were found hidden in a consignment of sugar.
"The world needs to sit up and take note: you cannot go around shipping undeclared weapons of war through the Panama Canal," he told Radio Panama listeners.
Weapons seized on board North Korean ship. Image from Martinelli's Twitter account
"We had suspected this ship, which was coming from Cuba and headed to North Korea, might have drugs aboard so it was brought into port for search and inspection," on the Atlantic coast of the country.
Initial reports said the ship was boarded last Friday.
"When we started to unload the shipment of sugar we located containers that we believe to be sophisticated missile equipment, and that is not allowed," Martinelli said.
The ship, named Chong Chon Gang, is being held as are the crew, who not only resisted the approach from the Panamanian authorities but attempted to sabotage the search, he said.
"The captain has tried to commit suicide, and the crew rioted" during the operation, the president said.
The boat was headed back to North Korea when it was stopped and taken to Manzanillo, east of the Atlantic opening of the Panama Canal, which is a major cargo distribution centre.
Cuba is the only one-party Communist regime in the Americas, and a rare ally of also-isolated Pyongyang.
The vessel "aroused suspicion by the violent reaction of the captain and the crew from Friday afternoon", Panama's Security Minister Jose Raul Mulino told the radio station.
And Javier Caraballo, an anti-drugs enforcement official, said: "Until now we have not found drugs in the boat, we found military equipment."
Presidential spokesman Luis Eduardo Camacho said later that "at first glance" the cargo appeared to include missiles, but an examination of the ship by specialists may take as long as a week.
North Korea defiantly carried out its third nuclear weapons test in February and then threatened to attack the United States, in language that was shrill even by its standards.
The North has for decades had a programme to develop missiles of all types. Last December it successfully launched a three-stage rocket which placed a satellite in orbit.
Pyongyang said the operation was a peaceful scientific mission, but the launch was widely condemned as a covert ballistic missile test banned under United Nations resolutions.
It is unclear whether the North has the technology to build a nuclear warhead for a missile.
UN sanctions bar the transport of all weapons to or from North Korea apart from small arms. Several of the country's ships have been searched in recent years.
In July 2009 a North Korean ship heading to Myanmar, the Kang Nam 1, was followed by the US navy due to suspicions it was carrying weapons. It turned around and headed back home.
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