Clashes between the group and the government forces in the province last week killed six Abu Sayyaf gunmen and four government officers. Six other rebels managed to escape.
Local media said Duterte flew to Bohol to attend a security briefing for the Association of Southeast Asian Nations (ASEAN) Summit, scheduled to be held in Bohol this week.
The Abu Sayyaf, founded in the early 1990s, has been engaged in high-profile kidnappings of local and foreign nationals.
The President asked the army to hunt down the group members, while declaring no plans towards a peace agreement with the group.-VNA