Abdusakur Tan, the governor of Sulu, told the Associated Press news agency that the attack may have been a diversionary tactic by the fighters following a deadly clash with Philippine soldiers earlier on Monday.
Surrounded by soldiers, police and about 600 armed civilian volunteers for days, the fighters tried to breach the cordon by opening fire, the military said.
At least two fighters were killed and nine soldiers wounded in the gun battle.
The incident prompted the soldiers to consider the use of force to rescue three aid workers believed to be held by them for four weeks now, the military said.
Hostages on film
The reports of the clashes came as footage of the hostages was aired on national television.
The three Red Cross workers - Andreas Notter of Switzerland, Eugenio Vagni, an Italian national, and Mary Jean Lacaba of the Philippines - were kidnapped on January 15 after inspecting a jail-water project in Jolo.
It is the first video released of the workers and was filmed by an undisclosed source.
|Kidnappings of foreigners are a regular occurrence in the southern Philippines [AFP]
They appeared unrestrained and seemed healthy.
Their abductors also appeared in front of the camera, and authorities were able to identify them as members of the Abu Sayyaf - long declared "terrorists" by the US and Philippine governments.
They have become widely regarded as a criminal bandit group rather than the rebel force they originally claimed to be.
But this latest kidnapping is seen as their attempt to redefine themselves.
"For years we've felt that the Philippine government has been trampling on our rights and controlling us," Abu Ali, an Abu Sayyaf leader, said in the video.
"If it's only us shouting, it's only us talking and we don't have a witness, if we don't take foreigners hostage, the government will not listen to us."
Philippine authorities say the Abu Sayyaf is not acting alone, and their sudden show of strength is because they are working with members of Jemaah Islamiyah (JI) as well as suspected Malaysian and Singaporean fighters.
Jemaah Islamiyah was responsible for the Bali bombings in 2002 which killed over 200 people, and two of those bombers are believed hiding with the Abu Sayyaf.
Maria Ressa, an analyst, told Al Jazeera that ideology is a reason why the Abu Sayyaf is seeking to justify its actions.
"It's a cause ... they are joining the 'Muslim brotherhood' in their eyes. So it's a kind of a moral imperative for them in that sense, [and] that's what JI gives them ... a kind of legitimacy that the Abu Sayyaf had lost for many, many years," she said.
"It was always the foreign influence that gave them ideological backing that made them feel they were part of a global movement."