A North Korean ship, caught in July while trying to move undeclared Cuban weapons through the Panama Canal, left on Saturday to Cuba, the Foreign Ministry said.
The Chong Chon Gang freighter departed from the Panamanian port of Colon with a crew of 32 on its way back to Cuba, the ministry said in a statement.
The ship got the green light last week to leave Panama after Pyongyang paid a fine of nearly $700,000.
Back in July, en route from Cuba, the ship was stopped on suspicion of carrying drugs as it tried to enter the canal, the busy waterway linking the Caribbean and Pacific.
April 12: Departs from Nakhodka in Russian far east, 200km east of North Korean border.
May 31: Arrives at Pacific side of Panama Canal.
June 1: Leaves the canal on the Caribbean side heading to Havana, but disappears from satellite tracking.
July 11: Reaches the Panamanian port of Manzanillo. It was later searched and the weapons were found.
September 26: Panama Canal Authority fines owners of the ship.
A search by Panamanian authorities uncovered 25 containers of Cuban military hardware, including two Soviet-era MiG-21 aircraft, air defence systems, missiles and command and control vehicles.
The containers were concealed under more than 200,000 sacks of sugar.
Both Havana and Pyongyang said the weapons were obsolete Cuban arms being shipped to North Korea for refurbishment under a legitimate contract and due to be returned to Cuba.
But neither country explained why the shipment was hidden if it was indeed legitimate.
The seized cargo has remained in Panama pending a court ruling on what to do with it.
The Foreign Ministry said that once the vessel arrives in Havana, it will be loaded with a shipment of sugar destined for North Korea.
Last month Panamanian authorities dropped charges against 32 of the 35 North Korean crew members.
The remaining three - the vessel's captain, first officer and political secretary - are still in custody in Panama, facing trial on arms trafficking charges.
The sailors on their way to Cuba "are happy because this affair in which they have lost seven months of their lives has finally come to an end," said a lawyer for the crew, Julio Berrios. He said they felt their long detention was unjust.
Panama asked the United Nations to send a mission to determine if the attempted shipment violated a UN embargo on arms deliveries to North Korea.
The results of the mission's probe have not been made public. But Panamanian authorities say the UN team's report confirms the cargo definitely violated the embargo.