MANILA (AFP) - Three people were killed as rescuers searched for at least three others still missing with more than a hundred rescued after a ferry sank in waters off the central Philippines, the government said on Sunday.

At least 110 people have been rescued after the sinking of the Maharlika II ferry on Saturday night, said President Benigno Aquino's spokeswoman Abigail Valte.

There had been some confusion over the number of people aboard the vessel when it went down but at least three were still unaccounted for, Valte said on government radio.

"They are trying to get a more precise number of the people who were on the vessel," she said.

Valte said the captain had told the coast guard there were 116 people on board when the vessel went down in bad weather, in contrast with earlier reports that there were only 84 passengers and crew on the manifest.

Valte said rescue boats were still searching for survivors at the scene of the sinking, about six nautical miles from the small island of Panaon, or about 680km south of Manila.

It was not clear why the manifest listed far fewer people but it is common practice in the Philippines for some passengers to board without being listed.

The vessel was hit by huge waves during bad weather worsened by the approach of Typhoon Kalmaegi to the northern Philippines, civil defence officials said earlier.

The ship took on water and went down as coast guard and private vessels rushed to pick up the survivors.

Poorly-maintained, loosely-regulated ferries are the backbone of maritime travel in the sprawling archipelago.

But this has led to frequent accidents that have claimed hundreds of lives in recent years, including the world's worst peacetime maritime disaster in 1987 when the Dona Paz ferry collided with an oil tanker, leaving more than 4,300 dead.