Cocaine, with a street value estimated at $2.5 million, was seized at the Port of Napier this week.
Customs officers intercepted 5kg of the Class A drug, which was concealed inside a refrigeration unit attached to a container, aboard the ship Cap Manuel on Tuesday night.
Initial testing of the powder substance showed a positive match for cocaine.
Customs manager drug investigations Mark Day said: "There has been an increasing prevalence of cocaine in illicit drug markets internationally and New Zealand is seen as part of those markets."
The ship, which had previously called at Lyttelton, left port at 8pm that day, its eventual destinations being Japan and China.
The cocaine was tightly packed into a bag, which is understood to have been discovered during a servicing of the container motor which had broken down.
The motors are essential in keeping the contents of the container cool and are regularly checked.
The find was immediately reported to port authorities and Customs officers notified.
The bag was taken from the ship by Customs to the No4 container storage shed where it was examined with assistance from members of the specialised police team.
Detective Inspector Ross Pinkham, the Eastern Police district manager of criminal investigation, said Customs and police were currently conducting a joint investigation to determine the origins of the packages and the background to the movements of the container.
"A conservative estimate places the street value of the drugs at nearly $2.5 million," he said.
The Napier cocaine stash is the third major seizure of the drug in the country this year.
On February 6, a 29-year-old American man was arrested at Auckland International Airport after Customs officers uncovered an estimated $1 million of the drug in two bottles of tequila.
The man arrived with little money and no plans for what he was going to do while in the country - raising suspicions.
Customs said it was the man's third visit to New Zealand in six months and that the amount of cocaine seized indicated he had some sort of network in place.
The man has yet to appear in court.
In early March, Customs staff at Auckland International Airport came across 2kg of cocaine.
Four men were arrested in relation to the haul after a joint operation between Australian and New Zealand Customs and police.
It was believed the cocaine stash was passing through New Zealand to be forwarded on to the lucrative Australian drug scene.
Australian Customs officers had seized about $18 million of cocaine, suspected to have been linked to the arrested men.