The yacht, two smaller boats and a vehicle were seized.
Marlborough Police said the three men were remanded in custody on charges of cultivating cannabis, possession of equipment to cultivate cannabis and possession of cannabis for supply.
The 45 year old and 51 year old were due to appear in Blenheim District Court today and the 64 year old on Thursday May 7.
Marlborough Area Commander Inspector Simon Feltham said the quantity and quality of the cannabis recovered suggested the men were involved in "well organised commercial activity."
The Drug Foundation said an ounce of marijuana usually cost around $300. At those prices, the stash in the yacht would be worth about $264,500.
However, the Weed Street Journal website said it was cheaper to buy cannabis in bulk.
Earlier this month, police told The Northland Age it had been a good cannabis growing season and huge commercial crops were seized.