Only two passengers remained missing Monday afternoon after nearly 1,000 were rescued following the sinking of a ferry in the southern Philippines, transportation officials said, according to The New York Times.

Nine people died in the mishap, officials said, adding that at least three of the fatalities — two adults and a 2-year-old boy — occurred in the scramble for safety.

Authorities were still investigating the cause of the sinking of the vessel, Superferry 9, which went down early Sunday morning.

Passengers interviewed by radio stations in Manila said they did not hear an explosion prior to the sinking, and weather did not appear to be a factor. The ferry was bound from General Santos City in the south to Iloilo City in the central Philippines.

Officials said Monday that all the vessels of Aboitiz Transport System, the country’s largest operator of passenger ships, could be grounded pending the completion of an “audit inspection” by the Maritime Industry Authority and the Philippine Coast Guard, according to Thompson Lantion, an undersecretary with the authority.

The rescued passengers would receive “assistance such as medical, hotel accommodation and transport needs,” according to Jess Supan, the vice president for safety and security for Aboitiz.

Also on Monday, maritime officials said a cargo ship, the MV Hera, sank Sunday in waters off the central Philippines. The crew — four South Koreans and 15 Filipinos — was rescued after drifting for hours in an inflatable life raft, the coast guard said. The vessel was en route to China when it went down.

The previous day, not far from the Superferry 9 incident, a boat in Basilan capsized, officials said. All 28 passengers, most of them women and children, were rescued.

Superferry 9 has had a string of seagoing mishaps, forcing the maritime authority to suspend it from service in 2007 over safety issues.

In May, the ship was stranded at sea for more than 12 hours because of engine trouble, government officials said at the time. But Mr. Supan said the ship had been in good shape.

“It wouldn’t be allowed to leave the port if there’s any deficiency,” he said, according to ABS-CBN television.

The Philippines, a typhoon-prone archipelago of more than 7,100 islands, is notorious for its sea disasters, often caused by some combination of tropical storms, poorly maintained boats and weak regulation.