Troops overran the jungle lair of Al Qaeda-linked Abu Sayyaf militants in the troubled southern Philippines, killng five of the guerrillas, according to the military.

Regional military spokesman Lieutenant Colonel Randolph Cabangbang said the army offensive on remote Basilan island on Saturday also left two soldiers dead.

"The firefight lasted for three hours," Cabangbang said in a brief statement sent to news agencies on Sunday.

He said the Abu Sayyaf militants, numbering around 30, abandoned the small rebel encampment of seven bunkers, communications equipment and ammunition.

One of the five gunmen killed was believed to be Juhaiber Alamsirul, a known 'sub-commander' of the Abu Sayyaf, who operates mostly on Basilan island and has been linked to previous kidnappings in the area.

The Abu Sayyaf is a 300-strong gang of self-styled Islamic militants.

It was set up in the 1990s by a Filipino Islamic firebrand using seed money from Osama bin Laden's Al Qaeda network, local and western intelligence groups said.

The Abu Sayyaf is blamed for the country's worst terrorist attacks, including the bombing of a passenger ferry in Manila Bay in 2004 that killed over 100 people.

It was also behind a string of high profile abductions targeting foreign and local tourists, traders and missionaries in the south, authorities said.