The yacht was intercepted off the cost of southwest Cornwall and escorted to Newlyn.
Newlyn harbour was sealed off temporarily by police for “public safety” reasons following the seizure – but was later re-opened.
Images from the scene show NCA officers unloading a large amount of drugs from the yacht named Marcia following the seizure.
A specialist bomb squad also went the scene as part of the investigation.
Members of the National Crime Agency are leading the operation with the support of UK Border Force and Devon and Cornwall Police – who remain at the site.
An NCA spokesman said: “As part of a National Crime Agency-led operation, the Border Force cutter HMC Vigilant intercepted a sailing yacht of the south west coast of Cornwall and escorted the vessel into Newlyn harbour where it arrived yesterday (Thursday 20 July).
“Two men have been arrested for drug trafficking offences and are now being questioned by NCA officers, who are leading the investigation.”