The Saint Thomas of Aquinas was believed to be carrying 692 passengers and crew members during the accident, and "less than 100 people are still missing," said Joy Villegas, a coast guard information officer.
"Search and rescue operations will go on throughout the night," she said. "We are hopeful we would find more survivors, since the accident occurred near the shoreline."
Coast guard and Navy ships, local fishermen, police and emergency workers were scouring the waters near the accident site, which was 2.3 nautical miles from the shoreline, Villegas said.
But "rescue operations are being hampered by zero visibility," said Chief Superintendent Generoso Cerbo Jr, a regional police director. "It`s very dark in the area."
Most of the passengers were already sleeping when the accident happened, survivors said.
"We were jolted from sleep and commotion broke out," Glenda Sabilla told a radio station in Cebu City. "Everyone frantically searched for life vests and we all started to jump off the sinking vessel."
Another passenger, Jerwin Agudong, said he saw some people trapped in the ferry.
"There were people who were not able to get out," he told a Manila radio station. "Others who jumped into the water were injured."
The Saint Thomas of Aquinas was travelling to Manila via Cebu City from the southern province of Agusan del Norte when the accident occurred, said coast guard vice commandant Rear Admiral Luis Tuason Jr.
The Sulpicio Express was travelling from Cebu City to the southern city of Davao, he added.
Sea travel is a key mode of transportation in the Philippines, an archipelago of more than 7,000 islands. But accidents are common due to poor safety standards and overloading.
The country was the site of the world`s worst peacetime maritime disaster when a ferry collided with an oil tanker days before Christmas in 1987, killing more than 4,300 people.
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