Southern military commander Maj. Gen. Ernesto Carolina told the AP one of the gunmen, believed to be Sabaya, was fired at from only three yards away.
Carolina said he had no doubt that Sabaya was dead.
Abu Sayyaf on the Run
Sabaya was the leader of a predawn raid on a resort on May 27, 2001, in which the Abu Sayyaf took 20 hostages, including the Burnhams and another American, Guillermo Sobero of Corona, Calif. The group later beheaded Sobero.
The massive search that followed led to the ongoing six-month deployment of 1,000 American troops to train local soldiers to combat Abu Sayaaf terrorists. U.S. Defense Secretary Donald Rumsfeld has approved a plan to let those U.S. special operations trainers go out into the jungle with the Philippine military on the hunt for the Muslim guerrillas.
The U.S. military provided planning, intelligence and communications for this latest operation, helping target the boat. Asked whether Americans were nearby, Sater told the AP: "Yes, but I can't say how near."
Pentagon officials say hundreds of Abu Sayyaf have been killed, detained or fled the country since the United States began the training operation in February. They are believed to be demoralized, low on supplies and running out of places to hide.
Sabaya's real name was Aldam Tilao. He once studied computer engineering, but after visiting Saudi Arabia for work, he returned home in the late 1980s and later disappeared.
ABCNEWS' Brian Hartman at the Pentagon contributed to this report.