After a US Customs and Border Agency aircraft spotted the 30-foot boat off the US island territory, a Lynx helicopter from the HMS Lancaster and a high-speed pursuit boat intercepted the vessel and collared the three suspected smugglers aboard.
The 1,499-pound stash of cocaine was recovered by Royal Navy divers after the three men threw it overboard.
The men were subsequently handed over to Puerto Rican authorities and the boat was sunk by Royal Navy gunfire in keeping with standard practice.
“We have all trained really hard to get where we are and have a fantastic relationship with the US coast guard guys. It is an amazing feeling to get such a great bust and stop millions of pounds worth of cocaine hitting the streets,” said Able Seaman James Duffy, coxswain of one of Lancaster’s sea boats, according to the ministry statement.
Defence sources said the cocaine was thought to be destined for the United States.
The Caribbean is recognised as a prime smuggling route for drugs heading from Central and South America to the US, or onwards to Europe.
The US Coast Guard has seized 45,200 pounds of cocaine and 8,500 pounds of marijuana during 22 operations in the past year, according to the UK ministry.
HMS Lancaster’s seizure was its third in three weeks. Britain’s Ministry of Defence said the ship had earlier intercepted marijuana with a street value of about £700,000 and stopped another vessel with a significant amount of cocaine and heroin onboard