The HMS Montrose Lynx helicopter spotted the craft during one of her dawn patrols.
Snipers then sank it with heavy machine gun fire "in full view of the pirate camp", a Nato statement said.
The boat was identified as the whaler from the MV Zouflecar, a vessel which has been acting as a pirate "mother ship" since it was seized on November 3.
"Our destruction of the whaler close to a known pirate camp has sent a message to the Somali pirates, that NATO and other coalition forces are willing to take the fight to them in order to prevent them attacking merchant ships," said Montrose's commanding officer, Commander Jonathan Lett.
Nato and EU Navfor, the European Union Navy Force Somalia, have intercepted several suspected pirates off Somalia and in the Gulf of Aden over the past few weeks, disrupting potential attacks.
A helicopter from an unidentified warship helped a Norwegian bulk cargo ship to escape an attack by pirates in the
Indian Ocean.
The Carmencita was sailing from Australia to the Red Sea when it was attacked by pirates and sent a distress signal, which the warship received and sent the helicopter to scare off the attackers.
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