Government forces conducted a major offensive against the group of Moro National Liberation Front (MNLF) founding chairman Nur Misuari on Monday.
The Armed Forces of the Philippines said troops have pushed back Misuari's men to the shoreline of barangay Santa Barbara in Zamboanga City.
Government also said they been able to take control of the grand Masjid Mosque, which MNLF fighters used as a hideout the past few days.
Authorities said 51 of Misuari's men have allegedly been killed and 70 others have been captured.
Interior and Local Government Secretary Mar Roxas said it's difficult to say how many hostages are still being held. Over the weekend., police had estimated the figure was down to seven from a high of around 200.