"This operation is part of our campaign to flush out the Abu Sayyaf which is responsible for a series of kidnappings," she told the AFP news agency.
But Mohagher Iqbal, the chief negotiator for the Moro Islamic Liberation Front (MILF), a group fighting for a separate homeland for Filipino Muslims, told Al Jazeera that Abu Sayyaf members were not in the area and not involved in the clashes.
"Three men from our forces were killed, and this was clearly a military offensive against our forces in Basilan," he said.
"The situation will escalate if the military do not stop these attacks"
Moro Islamic Liberation Front
"There was no Abu Sayyaf in our area. The military provoked and attacked our forces. The MILF is on defensive mode and the situation will escalate if the military do not stop these attacks."
Philippine military commanders say they believe that the Abu Sayyaf is being supported by the MILF.
The MILF formed as a breakaway group in 1977, when it split from the Moro National Liberation Front (MNLF), which had called for an independent Islamic state a decade previously.
Following the split, the MNLF subsequently entered into negotiations with the government in Manila and signed an agreement a decade later relinquishing its stated goal of independence.
But the 12,000-strong MILF continue to fight for political autonomy and the group is one of four fighting for a separate Muslim state in the southern Philippines.
The Abu Sayyaf split from the MNLF in the early 1990s and US intelligence agencies believe the group has ties to Osama bin Laden's al Qaeda network.
Abu Sayyaf fighters are particularly active on Basilan island, and although mainly known for kidnappings for ransom, the group has also admitted responsibility for a series of bomb attacks, including an attack on a ferry in February 2004 that killed more than 100 passengers.