The latest attack was led by al-Qaida-linked Abu Sayyaf gunmen and other militants, officials said.
They planned to set fire to a village and a wharf on the rural outskirts of predominantly Christian Lamitan city on Basilan island.
The attack was repulsed by government forces in an hour-long clash that left a government militiaman and an unspecified number of militants dead, and two soldiers wounded, army Col. Carlito Galvez said.
The Moro rebels joined the Abu Sayyaf in today's attack. Galvez said that the Abu Sayyaf, which is a violent faction of the Muslim separatist rebellion, was trying to take advantage of the hostage standoff in Zamboanga "to try to improve its influence and mass base support."
Another government militiaman was missing and troops were pursuing the attackers, who were led by wanted Abu Sayyaf commanders Isnilon Hapilon and Puruji Indama, Galvez said.
Regional Gov. Mujiv Hataman said that authorities had discovered the planned assault in Basilan, allowing them to monitor rebel movements and evacuate residents as early as yesterday.
In Zamboanga, government troops, backed by armored troop carriers, engaged the rebels in a fierce exchange of gunfire in Santa Catalina village, where the insurgents were holding some of their hostages, igniting a blaze that gutted about 30 houses.
The four-day crisis has virtually paralyzed Zamboanga, a lively trading city of nearly a million people, with most flights and ferry services suspended.
Communities near the clashes resembled a war zone, with armoured troop carriers lining streets, troops massing at a school and snipers taking positions atop buildings. A mosque and its minaret were pockmarked with bullet holes.
More than 15,000 villagers have fled the fighting and took shelter at schools and a grandstand in a seaside sports complex.
Troops were under orders to prevent the rebels from straying beyond the communities they seized or getting reinforcements, Interior Secretary Mar Roxas said.
