"It is a flagrant violation of safe passage through the Panama Canal and we have little tolerance for this kind of activity," canal administrator Jorge Quijano said.
"It is going to be sanctioned," he said, adding that authorities were still mulling the size of the fine.
"It's obvious that there were containers that had not been declared, not to mention what was inside them."
The ship, the Chong Chon Gang, was boarded and searched July 10 on suspicion it was smuggling drugs.
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Havana said they were obsolete Cuban arms being shipped to North Korea for refurbishment under a legitimate contract.
A team of UN experts is in Panama to inspect the weapons and determine whether the shipment violated a UN ban against arms transfers to North Korea.
Quijano said fines imposed by the canal authority range from USD 10,000 to USD 100,000 for serious violations and up to USD 1 million for "very serious" violations.
Warships and ships carrying military or nuclear material routinely go through the canal, allowed passage even at times of war.
The only requirement is that canal authorities be given prior notice so that local authorities can take appropriate security precautions.
With five per cent of the world's trade passing through it, the canal is a strategically important chokepoint requiring tight security procedures.
Only four North Korean flagged vessels have transited the 80-kilometre canal in the past two years.