"We have information that South Philippines will become (an ISIS base). We will strengthen, increase alertness in the border areas," BNPT chief Suhardi Alius said here on Tuesday.
The agency, he said, will work to prevent weapons smuggling, spread of ISISs ideology, and other undesirable threats.
BNPT has alerted the public and called on them to stay away from any radicalism.
Previously, Defense Minister Ryamizard Ryacudu said that ISIS planned to develop a base in the South Philippines, and called on the public to become more alert.
"I just returned from the Philippines yesterday. I already said six months ago that (the terrorist group) will expand. (The situation) must be closely monitored," he said here over the weekend.
He suggested that ISISs plan to establish a base in the Philippines must be thwarted as its activities could affect regional order and national security.
The move could threaten the cohesiveness, unity, and integrity of the Indonesian nation both at home and abroad.
ISIS has declared that it will build a base in the southern Philippines as part of its efforts to create a new caliphate in the Philippines, Indonesia, Malaysia, and Brunei Darussalam.
The headquarters in the Philippines is relatively close to Tarakan, Kalimantan, and Poso, where a number of Islamic terrorists are still at large.
Philippines President Rodrigo Duterte has also warned of ISISs plan to establish a base in the Philippines to run its operations in the region.(*)