Foreign naval forces launched a second raid to destroy a suspected pirate "mother ship" near Hobyo on the Somali coast that they had attacked 24 hours earlier, witnesses said on Friday.

"A military helicopter attacked a boat near Hobyo last night (Thursday). It opened fire on the boat and completely destroyed it but there was no casualty," Abdulahi Jama, a witness, told AFP from Hobyo.

"The boat had been attacked and damaged the night before (Wednesday) when several of its crew were killed but the chopper returned and burned down the boat which had already drifted back to shore," Ahmed Yusuf, a fisherman in Hobyo said.

Witnesses could not identify the helicopter gunship's nationality but believed it was one of the foreign navies patrolling waters off Somalia as part of an anti-piracy operation.

The attack on Wednesday evening left at least four dead and six wounded according to pirate sources who spoke to AFP.

Ecoterra International, an environmental and human rights organisation monitoring maritime activity in the region, confirmed Thursday night's attack.

"The naval helicopter gunship returned, firing two missiles and opened up with heavy nachine-gun fire ... on the vessel," Ecoterra said in a statement.

"The identity of the dhow was established by our local observers as FV AL AFINIYA, which had been trailed by the navies," the group said, confirming that at the time of the second attack no one was on the vessel and there were no further casualties.

A local pirate told AFP the targeted boat was being used by the pirates to bring supplies to another hijacked vessel moored off the coast.