Brigadier-General Alexander Aleo, a military spokesman, said the motive for the shootings on Friday is still unknown but could trigger fresh tension between Christians and Muslims before US counter-terrorism drills at the end of the month.
A survivor of the attack told soldiers who rushed to the area that the gunmen had asked them whether they were Muslims or Christians before firing their weapons.
Aleo said three men, two women and an eight-month-old infant were killed. Six others, three of them children, survived with minor injuries
About 200 Muslim activists marched around Jolo town on Thursday, demanding that US commandos taking part in annual drills leave. They also burnt American flags.
Every year, about 5000 US troops take part in war games throughout the Philippines.
Protesters said they had seen some US troops fighting alongside Philippine soldiers in November during offensives against the Abu Sayyaf, a Muslim group with ties to al-Qaida and the regional network Jemaah Islamiah.