An Indonesian navy boat comes into port after searching for survivors from the Teratai Prima, which sank in a cyclone over the weekend. (Associated Press)

Waves and driving rain from a cyclone that capsized a ferry off Sulawesi Island in Indonesia were hampering rescuers' efforts as they searched for more than 250 missing people on Monday.

Most of the passengers were sleeping onboard the Teratai Prima when it was struck by Cyclone Charlotte on Sunday and sank about 50 kilometres off the coast of western Sulawesi, officials said.

The 700-tonne vessel was carrying passengers and cargo from Parepare to Samarinda on the Indonesian half of Borneo.

Three warships, airplanes and a helicopter were deployed on Monday but were hampered by driving rain, strong winds and waves, said Col. Jaka Santosa, who was heading the rescue operation.

An Indonesian man looks at a passenger list and photos of potential victims of the ferry sinking in Indonesia. (Associated Press)

No survivors or bodies had been recovered by the military rescue operation on Monday, despite patrolling the Makassar Strait for hours, Santosa, said.

Eighteen passengers and four crew members were rescued from the sea by fishermen before the military launched its search operation at daybreak, Transport Minister Jusman Syafi'i said.

Survivors who were taken to the port of Parepare on Monday said the ferry had been slammed by four-metre waves.

"People were screaming, 'Help, help!,'" said survivor Sampara Daeng Gassing, 35, who clung to a tire for two hours in the pounding storm but lost his nine-year-old son and father-in-law.

"I lost hold of my son and my father-in-law when a big wave hit me," Gassing told the Associated Press.

Passenger count uncertain

About 250 passengers and 17 crew were believed aboard the ship, officials said. But passenger lists for ferries in Indonesia can be inaccurate because tickets are frequently sold on board and not properly tallied.

Officials believe about 150 people may have jumped from the ship before it sank.

Rustam Pakya, head of the Health Ministry's crisis centre, told Reuters that survivors have confirmed the deaths of at least six people.

"There is a great possibility that many more died than we expected because it happened when they were sleeping," Taufik Bulu, an official with maritime safety, told Reuters.

The captain, who survived, is being investigated for allegedly ignoring warnings from the Indonesian weather agency that conditions on the crossing were too dangerous, Djamal said.

"We will investigate thoroughly why the captain decided to go," he said.

Officials said it does not appear a general alarm was raised to warn the passengers before the sinking, based on interviews with the survivors.

The captain told officials the boat sank so quickly that the crew did not have a chance to tell the passengers to put on life-jackets, Djamal said.

The National Transportation Safety Committee said the Teratai Prima was inspected on Dec. 9 and found to be in good condition. Initial findings are suggesting that the sinking was caused by the weather and not a mechanical problem, said Abdul Gani, the Transport Ministry's top official for sea transport.

With files from the Associated Press