Two military aircraft launched the attacks in Zamboanga.

The raids follow a recent wave of violence in the region in which 35 people have died.

Philippine President Benigno Aquino is under pressure to end a ceasefire with the rebels, but says he wants to find a peaceful solution.

The rebels, from the Moro Islamic Liberation Front (MILF), are known to be hiding in the area which was attacked by the military.

"About 100 heavily armed bandits are holed up in their bunkers and running trenches," said another army spokesman, Major Harold Cabunoc.

The MILF has been fighting for an autonomous Muslim homeland in the Philippines, which is a mainly Roman Catholic country.

The group has been involved in sporadic peace talks with the government since 2003 and has held a ceasefire since 2008.

However, renewed violence has flared in October.

Last week, 19 soldiers were killed on the island of Basilan and three others died over the weekend, along with five plantation workers.