Sonny Boy Hamsain was arrested in Isabela City on Basilan island, the stronghold of the Muslim extremist Abu Sayyaf group, said Lt. Col. Fredesvindo Covarrubias, head of the militarys civil relations group.
Hamsain, who is employed by the Basilan Dock Handlers Corp., was arrested at the wharf by a five military intelligence agents and five members of the Citizens Armed Forces Geographical Unit (CAFGU) last Wednesday.
Covarrubias said the suspect was in charge of collecting extortion money from traders in Basilan on Janjalanis behalf.
Hamsain carried a P300,000 bounty on his head stemming from murder and kidnapping charges, Covarrubias said.
Armed Forces Southern Command chief Lt. Gen. Roy Kyamko said Hamsains name was in the list of the countrys most wanted fugitives. He faces charges of double murder, multiple frustrated murder, and damage to property.
There is also a warrant for Hamsains arrest, issued by Isabela City Judge Danilo Bucoy, on charges of kidnapping and illegal detention.
Kyamko said initial interrogation disclosed that Hamsain had joined the Abu Sayyaf group sometime in 1992.
Haimsain denied the charges against him during interrogation following his arrest on Wednesday, according to a military statement.
Janjalani is one five Abu Sayyaf leaders wanted by the United States for the kidnapping and killing of two Americans in 2001 and 2002. Washington has offered a reward of up to $5 million for information leading to their arrest or conviction of the leaders.
It was not immediately clear if Hamsain was directly involved in the deaths of the Americans, or in the April 2000 abduction of 21 people, including Western tourists, from the Sipadan island resort in Malaysias Sabah state.
Hamsain will remain at the headquarters of the 24th Special Forces Company for tactical interrogation before he is turned over to police authorities, Kyamko said.
In 2002, more than 1,000 US troops trained Filipinos soldiers in a counter-terrorism campaign credited with helping cripple and dislodge the Abu Sayyaf from its Basilan strongholds. With reports from Jaime Laude