Extra troops have been deployed and security measures implemented to protect the polls on Basilan island from threats by Abu Black, an Abu Sayyaf commander, Col. Rey Ferrer said.
Ferrer said Abu Black had been intimidating people in the towns of Tipo-Tipo and Sumisip. Abu Sayyaf has been linked to al-Qaeda by the United States and has been accused of planning bombings in Manila to disrupt the polls.
"Intelligence reports said the rebels were planning to attack and disturb the national elections on Monday. We are now on red alert," Ferrer told reporters in Basilan.
The Philippines is holding general elections on Monday for the presidency, parliament and local government.
The Abu Sayyaf have built up a fearsome reputation in the past decade in the southern Philippines following a series of bombings and kidnappings, mostly targeting foreigners and Christians.
Members of the group have also been known to hire themselves out as enforcers for local political warlords.