The military said people were leaving the mosque just a kilometer away from an Army camp when two men on a motorcycle indiscriminately opened fire with an assault rifle and a pistol.
Brig. Gen. Alexander Aleo, head of the Southern Command anti-terror task force, said the military counted at least 10 people wounded.
But an Islamic non-government organization, the Suara Bangsamoro, said it counted 20 casualties who were brought to the provincial hospital.
"They had just finished prayers when they were attacked in the mosque," Suara Bangsamoro spokeswoman Amira Lidasan said.
Aleo said a manhunt for the perpetrators had been launched, but said the motive for the attack was unknown.
The suspects escaped toward downtown Jolo and sped to an unknown destination, he said, citing reports.
Aleo said military intelligence agents were deployed to help the police investigate the incident.
"The attack is senseless and an act of cowardice and we condemn whoever the perpetrators are," he said.
Aleo dismissed a report that a soldier had attacked the mosque in retaliation for the killing of a Marine trooper two weeks ago.
Military sources believe the attack was aimed at disrupting the upcoming "Balikatan" military exercises in Sulu where US and Filipino troops are to conduct humanitarian and engineering missions.
"It is a desperate move to revive the anger of the Muslims to draw support in opposing the Balikatan here," a military intelligence source said. — Roel Pareño, AFP