Britain's Ministry of Defense revealed that a small vessel, suspected of being involved in an attempted hijacking of a Danish cargo ship, was intercepted in the Gulf of Aden.
Crews launched from the HMS Cumberland exchanged fire with the boat, which was believed to be Yemeni, before they boarded the craft.
"Two foreign nationals, believed to be Somali pirates, were shot and killed in self-defense," a Ministry spokesman said.
"A Yemeni national was also found injured and later died, despite receiving emergency treatment from the ship's doctor. It is unclear whether his injuries were as a result of the fire fight or a previous incident involving the pirates."
The fatal shootings are reportedly the first taken at sea by the Royal Navy since the Falklands war.
The HMS Cumberland is part of NATO-led patrols fighting piracy in the Gulf of Aden, which is a key shipping lane leading to the Suez Canal.
The number of pirate attacks in the region has surged this year, according to the International Maritime Bureau.