He singled out the predominantly Christian province of Papua as one of the few exceptions.
"These sleeper cells can easily join up with other radical cells," he said.
Governments across the region have been on high alert since ISIS -linked terrorists, mostly from Southeast Asian countries, overran a city in the southern Philippines about three weeks ago.
The Philippine military, which has carried out air strikes and raids in Marawi city, said on Tuesday the terrorists still control about 20 percent of the city.
Indonesian and Malaysian officials have stepped up security to prevent militants from escaping from Marawi over their shared borders with the Philippines.
"It's easy to jump from Marawi to Indonesia and we must all beware of sleeper cells being activated in Indonesia," Nurmantyo said.
Singapore said on Monday it had detained an assistant child-care worker suspected of trying to join ISIS, the first woman to be held on such charges in Singapore.
A gun-and-bomb attack that killed four people in Jakarta last year marked the first ISIS strike in the region.
There has since been a string of small, ISIS-inspired attacks in Indonesia, the latest of which were twin suicide bombings at a Jakarta bus station that killed three police officers last month.
(Reporting by Agustinus Beo da Costa and Ed Davies; Writing by Kanupriya Kapoor; Editing by Paul Tait)
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)
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