Susilo Bambang Yudhoyono made the remarks at the opening of a two-day meeting of Asia-Pacific religious leaders in Yogyakarta in central Java.
"There is one exceedingly heinous form of violence that we must grapple with, and that is the scourge of terrorism," the state-run Antara news agency quoted Yudhoyono as saying.
"To my mind, terrorism today must be regarded as the enemy of all religions."
Indonesia has been hit by a series of terrorist bombings in the past few years, including the Oct. 2002 Bali blasts, the Aug. 5, 2003 bombing of Jakarta's J.W. Marriott Hotel, and the Sept. 9 bombing outside the Australian embassy in Jakarta. The three attacks killed 224 people.
Indonesia and Western countries have blamed the al-Qaida-linked regional terror group Jemaah Islamiyah for the attacks. Indonesian police rounded up more than 150 Muslim militants following the Bali bombings.