Migrants seeking asylum in Australia hijacked a Sri Lankan fishing boat and threw its crew into the open sea to die, a survivor said.

Two fishermen floated for hours before they were rescued by two merchant ships after Tuesday's ordeal off southeastern Sri Lanka, said Roshan Kumara from the southern fishing village of Kudawella. They were admitted to the hospital to be treated for cuts and other injuries.

Three crew members have not been found, nor has the hijacked boat.

Kumara said Thursday the leader of his fishing boat collaborated with the attackers and discussed their plans to go to Australia. Later they beat up the fishermen and threw them into the sea where they managed to float for hours until their rescue.

Police spokesman Prishantha Jayakody said four people have been arrested on shore accused of helping plan the hijacking. There were about 10 would-be illegal migrants on the boat, he said.

Sri Lanka's navy has arrested hundreds of people travelling illegally to Australia over the past months. The journey often takes migrants to Indonesia before they set sail for Australia.

Australia is struggling to stop a surge of would-be refugees from poor or war-torn countries including Afghanistan, Iran and Sri Lanka. Hundreds have died while attempting the voyage over the past year.