The two men, La Utu bin Raali and La Hadi bin La Adi, were kidnapped by the terrorist group on 5 November 2016 from different vessels at that time, while sailing in Malaysia's waters of Sabah, according to local media.
"The release of the two hostages was resulted from excellent orchestrated cooperation between several institutions, particularly the national military and intelligence agency," Xinhua news agency quoted Indonesian Foreign Affairs Minister Retno Marsudi saying at the event.
However, the ministry did not explain how the two hostages were released from the terrorist group.
According to data provided by the ministry, 32 Indonesian were kidnapped by Philippine terrorist groups since 2016, of which 29 have been released so far. Indonesian authorities are still working to free the remaining three hostages.