Ramil Vela and Buboy Letriro were captured by the group on June 12 along with Jordanian journalist Baker Atyani, who was not released with Vela and Letriro Saturday night, GMA News Online reported.
Autonomous Region in Muslim Mindanao Police Chief Noel Delos Reyes said: "Last night they were recovered from a hotel they were staying," adding, "I think they will be flown back to Manila."
"The two are now under protective custody of the Sulu provincial police office," Delos Reyes said.
Police and military officials did not comment on Atyani or his fate, China's Xinhua News Agency reported.
Philippine army spokesman Randolf Cabangbang said Vela and Letriro told police they had not seen Atyani since a week after they were kidnapped.
Abu Sayyaf, founded in the 1990s, is a Muslim terrorist group that often engages in kidnappings for ransom, as well as bombings, beheadings, assassinations and extortion.
Its stated goal is to create an independent Islamic state in western Mindanao and the Sulu Archipelago areas in the southern Philippines.