MOGADISHU (AFP) -A US warship shelled suspected Al-Qaeda targets in northeastern Somalia after Islamist fighters clashed with troops from the country’s semi-autonomous region of Puntland, officials said Saturday.

The US Navy destroyer fired on several targets overnight in mountainous and remote areas outside the coastal town of Bargal, where Islamist militants are believed to have bases.

“The US military was targeting the Al-Qaeda hideout. This was aimed at flushing out all the terrorists,” said Mussa Jelle Yusuf, the governor for Barri region.

“Puntland troops are surrounding the Bargal hills and hunting for those Al-Qaeda elements. They … will be captured or killed,” he added.

US Defence Secretary Robert Gates refused Sunday to comment on the reported bombardment, saying it was “possibly an ongoing operation.”

“I think that’s possibly an ongoing operation and I’m not going to be able to talk about that,” Gates told reporters in Singapore where he is on a visit.

A top Somali government official in Mogadishu said there were fatalities from the US shelling, but could not give the exact figure.

“There are deaths from the attacks, but we do not know the exact number because of the remoteness of the area,” said the official, who requested to anonymity.

A Puntland military official said the operation came three days after the arrival of Islamist fighters and foreigners of Arab origin in Bargal, about 1,250 kilometres (780 miles) northeast of the Somali capital Mogadishu.

“Our forces have fought with Islamic fighters, including foreigners linked to Al-Qaeda,” said the official, who requested anonymity.

“After the fighting a US Navy ship shelled three targets on the outskirts of Bargal in the mountainous area.”

“We cannot get information on casualties, but the shelling continued for hours… The Puntland troops are still chasing Islamic fighters in the mountainous area,” he added.

On Wednesday, Puntland said its troops had killed at least two foreign fighters who had sailed into Bargal.

“These are Al-Qaeda fugitives who fled from the southern part of Somalia. We do not know the motive of their arrival here, but it is definitely terrorism-related,” Yusuf said.

The US Defence Department refused to confirm the raid, but vowed to keep pursuing extremists.

“We recognize the importance of working closely with allies to seek out, identify, locate, capture, and if necessary, kill terrorists and those who would provide them safe haven,” spokesman Bryan Whitman said in a statement.

“The very nature of some of our operations, as well as the success of those operations, is often predicated on our ability to work quietly with our partners and allies.”

The CNN television channel reported that the destroyer was targeting a suspected Al-Qaeda operative believed to have been involved in the 1998 attacks on US embassies in Kenya and Tanzania that killed 224 people.

A US force is based in Djibouti and patrols the Indian Ocean and the Gulf of Aden with the aim of reducing the threat of terrorism.

Earlier this year, a US aerial gunship bombed positions in southern Somalia after Ethiopia-backed Somali government forces ousted a powerful Islamist movement from the country’s southern and central regions. Local elders said more than 100 civilians were killed.

The targets were suspected Al-Qaeda operatives blamed both for the 1998 US embassy bombings and the 2002 suicide attack on an Israeli-owned hotel in the Kenyan port of Mombasa, that killed 15 people.

Among the so-called “high value” Al-Qaeda militants believed to be in Somalia are Fazul Abdullah Mohammed from the Comoros, Kenyan Saleh Ali Saleh Nabhan and Sudanese national Abu Taha al-Sudani, an arms expert close to Osama bin Laden.

Others are Sheikh Dahir Aweys, the hardline cleric heading Somalia’s Islamic Courts Union, and Adan Hashi Ayro, the commander of the Islamists’ militia wing, the Shabaab.

US intelligence says Al-Qaeda has stepped up operations in Somalia, a nation of about 10 million people wracked by lawlessness since the 1991 ouster of dictator Mohamed Siad Barre.

The US warship shelling raised fears in Mogadishu, where the government heightened security in anticipation of retaliatory attack.

“We are monitoring the situation,” a top security official told AFP.

Northern Somalia’s Puntland and neighbouring Somaliland, which have declared a form of autonomy, have enjoyed relative stability compared to Somalia proper.

Puntland president Adde Mussa said Al-Qaeda planned attacks in northern Somalia, which has been spared the recent heavy fighting between Somali government forces and Islamist and clan insurgents.