The residents came from three towns on Jolo island, 1,000 kilometres south of Manila, and four towns in nearby Basilan province where troops have fanned out to hunt down Abu Sayyaf rebels and Jemaah Islamiyah (JI) militants.
The Office of Civil Defence said a total of 7,474 people have fled their homes in the towns of Indanan, Parang and Maimbung on Jolo since fighting broke out between the military and the insurgents last week.
In Basilan, 10,794 civilians have been forced to evacuate their homes in four towns, the office said.
The military is intensifying its operations against the Abu Sayyaf and the JI after suffering heavy losses in past weeks, including the killing of 25 soldiers in just one day of fighting on Jolo island last Thursday.
Last month, 14 marines were also killed in an ambush by separatist Moro Islamic Liberation (MILF) rebels in nearby Basilan province. Ten of the slain marines were beheaded and mutilated.
The MILF has disowned beheading or mutilating the marines, and an independent probe later blamed Abu Sayyaf rebels for the gruesome acts.
The military added that intelligence reports indicate that top JI militants Dulmatin, Omar Patek and Zulkifli bin Hir helped in planning the recent attacks on the armed forces.
Amid fears that the hostilities could jeopardize peace efforts in the south, President Gloria Macapagal Arroyo convened the National Security Council in Manila on Tuesday to brief senators, congressmen and other government authorities on the offensives.
She assured the council that the government was still pursuing peace negotiations with the MILF, adding that peace talks, which have been suspended since last September, were expected to resume in Malaysia on August 22.
She added the government was taking steps to protect civilians in battle zones and to ensure that the military strictly adhere to a 2003 ceasefire agreement with the MILF.
"It is imperative that we all work together without selfish politicking to preserve the peace we have achieved so far and to advance it toward a final agreement and the massive development that will follow," she said.
In the hostilities in Jolo, some members of the Moro National Liberation Front (MNLF), which signed a peace agreement with the government in 1996, were engaged in the fighting.
But the military stressed that the MNLF and the MILF were not being targetted in the offensives, stressing that the two main organisations were still supporting the government and that only breakaway groups were behind criminal acts.