Nine people died after the vessel capsized Sunday, CNN said. The remaining 957 had been rescued by Monday, the Coast Guard said.
Search crews were looking for the two still missing, CNN said. The Coast Guard said the SuperFerry 9, which left the city of General Santos on its way to Iloilo City, was not carrying any hazardous cargo.
It was the ferry's third major safety incident in three years, CNN reported, noting no deaths were reported in the 2006 and 2007 incidents.
The ferry sank off Zamboanga del Norte in the southern Philippines, The New York Times reported. Officials said among the nine fatalities, two adults and a 2-year-old boy died during a scramble for safety.
The cause of the incident was under investigation. Some passengers told Manila radio stations they did not hear an explosion before the ferry went under.
But Xinhua news agency quoted a survivor saying a sound similar to a minor explosion was heard in the lower portion of the ship before it started to tilt. However, seamen familiar with ferries told the Chinese news agency the sound could have come from sliding cargo hitting the hull.