The 90% pure drugs were so well hidden in the 65ft pleasure cruiser, the Louise, it took six days to find them.
They had originated in the Caribbean and were en route to the Netherlands. Dutch police have arrested six men.
They are thought to be an organised crime gang.
French authorities were alerted to the Louise while it was in the Caribbean in May and it was then tracked to Southampton, on its way to Holland.
Officials spent six days searching the vessel and found the drugs packed in a specially-designed compartment beneath the boat's bathing platform, UKBA said.
It is understood the cocaine, which originated in South America, was packed inside the boat while it was in Venezuela.
The average purity of cocaine seized at the UK border is 63%, officials said.
The haul is estimated to be worth about £50m wholesale and up to £300m on the streets.
Since the drugs were found in June, the UKBA has helped Dutch police track members of the gang and six men were arrested during early morning raids on Tuesday.
Two 44-year-olds were arrested in Amsterdam, a 60-year-old was held in Meppel, a 32-year-old and 34-year-old were arrested in Heusden, while a 27-year-old was held in Waalwijk.
A total of 100,000 euros (£87,300), two Harley Davidson motorcycles, two firearms, a silencer and a quantity of ecstasy were also seized.
Brodie Clark, head of the UKBA's border force, said: "This has been an enormous seizure of cocaine. This is the largest we have on record."
Asked about how the drugs were hidden, he added: "It was ingenious, it was difficult to find. Skilful people spent a number of days looking for it."
Immigration Minister Damian Green said: "UK Border Agency staff have shown vigilance, dedication and determination to uncover this shipment."