The Indonesians were granted their alien certificates of registration (ACRs) following a massive registration program by the BI.
Last February, the BI started processing the ACRs of some 2,000 undocumented Indonesians.
The bureau said it started the registration drive two years ago but only 1,500 Indonesians registered since most of them could not afford the P1,010 registration fee.
To encourage more undocumented Indonesian nationals to register, the Department of Foreign Affairs recently approved a move to lower the registration fee to P410 per registrant.
According to data from the BI, at least 70 percent of the Indonesians work as fishermen and farm workers in Glan town, Sarangani province; Jose Abad Santos town, Davao del Sur; and General Santos City, South Cotabato.
Immigration officials said many of the Indonesians had been living in Mindanao for the past five decades and are considered members of the community. They speak the local dialect fluently and some have children with Filipinos.