He also said that one marine had been wounded in the attack and noted that 15 assault weapons abandoned by the fighters had been seized.
Philippine forces have staged a number of assaults in recent weeks, acting on intelligence from captured fighters and US military surveillance.
The US has offered a $5m reward for the capture of Marwan, a US-trained Malaysian engineer Washigton says has links to several Southeast Asian armed groups with ties to al-Qaeda.
He has been accused by Philippine authorities of involvement in a number of deadly bombings in the country.
The US says he the leader of the Kumpulun Mujahidin Malaysia (KMM) and a member of the central command of Jemaah Islamiyah, which is blamed for numerous attacks, including the 2002 Bali nightclub bombings in Indonesia.
The group has been fighting for years to create an independent Islamic province in the Philippines.
Last month, Philippine forces killed Albader Parad, a young Abu Sayyaf commander, who has been accused of beheadings and high-profile kidnappings.
He was allegedly involved in the kidnapping of three Red Cross workers who were freed last year, reportedly after payment of a large ransom.