Authorities said a raid at the suspected hideout of Jamaah Islamiyah bomber Dulmatin on the remote southern island of Tawi Tawi early Friday only netted four children, a military rifle and other materials.
The children, flown to a military base for medical examination and safekeeping, were believed to be his, the Philippine Star reported.
The raid was conducted by Philippine Marines and commandos, but additional details were not disclosed.
Dulmatin is a prime suspect in the 2002 bombings on the Indonesian island of Bali. More than 200 people died in those attacks on restaurants and clubs frequented by Westerners, including scores of Australians.
Dulmatin, together with another operative of the Indonesian terror group, fled to the southern Philippines, where he has reportedly been hiding with the al-Qaida connected Abu Sayyaf group.
He is said to be an explosives expert trained by the Taliban in Afghanistan.
The United States has a $10 million price on his head as part of its Rewards for Justice program.
The Philippine military has been conducting an offensive against Abu Sayyaf and attempting to capture its leaders and Dulmatin since last last year.
An earlier raid resulted in the capture of Dulmatin's wife and two of their children.