Pirates caught redhanded by one of Her Majesty’s warships after trying to hijack a cargo ship off Somalia made the grave mistake of opening fire on two Royal Navy assault craft packed with commandos armed with machineguns and SA80 rifles.

In the ensuing gunfight, two Somali pirates in a Yemeni-registered fishing dhow were killed, and a third pirate, believed to be a Yemeni, suffered injuries and subsequently died. It was the first time the Royal Navy had been engaged in a fatal shoot-out on the high seas in living memory.

By the time the Royal Marines boarded the pirates’ vessel, the enemy had lost the will to fight and surrendered quietly. The Royal Navy described the boarding as “compliant”.

The dramatic confrontation, the latest in a series of piracy incidents in the Gulf of Aden in recent months, took place 60 miles south of the Yemeni coast and involved the Royal Navy Type 22 frigate, HMS Cumberland, which has a Royal Marine unit on board, on short-notice standby to engage in “non-compliant boardings”.

HMS Cumberland, on anti-piracy patrol as part of a Nato maritime force, detected the dhow which was towing a skiff, and identified it as a vessel which had been involved in an attack on the Danish-registered MV Powerful earlier yesterday. The pirates had opened fire on the cargo boat with assault rifles.

Under rules of engagement which allows the Royal Navy to intervene when pirates are positively identified, the commandos were dispatched from the frigate in rigid-raider craft and sped towards the pirates’ dhow. The Ministry of Defence said the Marines circled the pirates’ boat to try and persuade them to stop.

As they approached, however, several of the pirates, a mixed crew of Somalis and Yemenis, swung their assault rifles in their direction and opened fire. The MoD said the Royal Marines returned fire “in self defence”, and then boarded the dhow — a stolen Yemeni-registered fishing vessel.

The commandos found guns and other “paraphernalia” on board the dhow and a handful of terrified pirates. The MoD said it was unclear whether the Yemeni who died had been shot by the Marines or was wounded from a previous incident involving the pirates.

The gun battle was in stark contrast to the Royal Navy’s last encounter with a boatful of armed men - when crew members of HMS Cornwall, also a Type 22 frigate, patrolling in the Gulf in rigid raiders, were surrounded by heavily armed Iranian Revolutionary Guards in March last year. Eight sailors, including a woman, Leading Seaman Faye Turney, and seven Marines were taken hostage without a shot being fired, and detained for 13 days. The Commons Defence Committee described the incident as “a national embarrassment”.

Yesterday’s battle signalled a new policy of maximum robustness for the Royal Navy on the high seas. Captain Mike Davis-Marks, a senior spokesman for the Navy, said: “This is bound to have an impact on pirates who for the last two years have been getting away with seizing vessels and receiving large ransoms. Now suddenly there’s the threat of death and this may force them to think again, but they are determined people, so we’ll have to see.”

The Russians claimed a helicopter based on their own frigate Neustrashimy had also taken part in yesterday’s battle, though the Royal Navy knew nothing about it. The Royal Marine commandos who boarded the pirates’ dhow were supported by a Lynx helicopter from HMS Cumberland, the MoD said.