Immigration Commissioner Alipio Fernandez said the registration drive, which started early this year, is part of the bureau’s anti-terrorist campaign.
"It will then be easy for us to monitor the entry and stay of these Indonesians since those who will not register will be considered illegal aliens and are subject to arrest and deportation," he said.
Fernandez, however, said intelligence reports on the presence of some 10 JI members in Mindanao who have crossed the Philippine-Indonesia border still have to be verified.
He said immigration authorities in the South have been on alert since the Sept. 11, 2001 terror attacks in the United States.
Fernandez said Marines have been detailed with the bureau since 2002 to assist immigration agents in beefing up security in Zamboanga City and Brooks Point, Palawan.
According to the bureau, a total of 2,641 Indonesians in several Mindanao provinces have been issued their alien certificates of registration.
The bureau expects to register at least 3,000 more of the estimated 7,000 Indonesians by the end of the year.
Records show that majority of the Indonesians in Minda—nao have settled in the provinces of Sarangani, South Cotabato and Davao del Sur, in the towns of Glan and Jose Abad Santos and in General Santos City.
Fernandez said many Indonesians in Mindanao have inter-married and speak the dialects fluently.