THE seizure of a fishing boat that may have been preparing to set sail from Sri Lanka to Australia should be fully investigated, Opposition Leader Tony Abbott says.

Sri Lankan police said last night that three crewmen and the skipper of a trawler had staged a hijacking off the island nation on Sunday night to try to cover up the theft of the boat and use it for people smuggling.

Two crewmen were reportedly found bobbing in waters south of the island early on Monday.

The pair had initially told police that the trawler had been attacked by about 40 suspected illegal immigrants carrying swords who arrived in four small boats and overpowered the crew.

"There are conflicting accounts in their statements and it is now clear that this was an inside job to steal the trawler and possibly use it for an illegal journey to Australia," a senior police investigator said.

Mr Abbott told the Nine Network this morning: "It's very important that this matter be fully investigated.

"If people look to have committed very serious criminal offences on the way to Australia, well obviously people should be treated as those who have committed or at least allegedly committed criminal offences."

Mr Abbott said apart from fully investigating any suspected criminal activity, it should be made clear to asylum seekers that they could be staying at Australia's offshore processing centre at Nauru for a very long time.

"We have to have a system that has deterrents built in," he said.

Mr Abbott would not give a specific time frame, but said a coalition government would point out to asylum seekers they could be at the offshore processing centre for five years.

"People need to understand if they get on a boat to Australia, Nauru may not be just a brief detour on the way here," he said.

Mr Abbott refused to say whether he had talked to Indonesian president Banban Yudhoyono about the coalition's policy on turning back the boats.

"I don't conduct megaphone diplomacy," he said.

"They know exactly what we intend and I think they are comfortable with what we have in mind."

Opposition immigration spokesman Scott Morrison said the government's "mealy mouthed" no-advantage policy is not conveying a message of deterrence to the region.

"The government needs to stop tying itself in knots about its language over these things. If it's serious about no advantage, then they should say what it means," he told ABC radio.

"We should be clear that if you get on a boat and come to Australia, you should expect to wait up to around five years. That's the import of this policy."

The armed struggle aboard the fishing boat off Sri Lanka saw at least one crewman's throat cut.

With asylum pirates still believed to be at sea, Sri Lanka sent urgent alerts to Australia. However, after questioning crew, Sri Lankan authorities now believe the bloody fight may have been the result of a mutiny attempt.

Women and at least two young children were on board the vessel, which is still more than two weeks' travelling time from the Cocos or Christmas islands.

A merchant vessel captain who rescued one of two men who survived the ordeal last Sunday has revealed their hell after they refused to join the bid for Australia.

Loku Roshan and G.A. Suranga Sujeeve were bound - one was cut in the throat with a knife and stabbed in the stomach - before they were thrown overboard from the Theja.

MV Lusail's crew spotted the men on Monday and rescued one. Captain JA Petersen, of MV Edith Maersk, rescued the second.

The man rescued by Capt Petersen said he believed two colleagues had drowned, though Sri Lankan police said it was possible they were still aboard the Theja.

"He told us he was a fisherman from Sri Lanka and their fishing boat was attacked ... by some people who wanted their boat for emigration to Australia," Capt Petersen said.

"There were six people on this fishing boat. At least four of them were tied up and thrown into the sea.

"He told us that they were hurt by the pirates. They cut a big wound in his neck and stomach. We treated him."

The two men remain in hospital in the Sri Lankan city of Galle, police Supt Preshan Jayakody said.

He said the group of asylum seekers who took over the Theja declared: "We're going to Australia."

When Mr Roshan and Mr Sujeeve objected they were attacked, he said.

Four people have been arrested in Sri Lanka, and the smaller vessel used to reach the trawler was recovered.

The asylum seekers were all known to each other and the captain of the fishing boat, Supt Jayakody said.

"The captain had communication with this gang," he said. "We are trying to locate this boat.

"According to the statements of the two people who escaped they heard one lady, there were some babies - we believe two to three children.

"Some people, according to their version, said, 'We are going to Australia'."

A spokesman for Immigration Minister Chris Bowen said the minister had spoken to Sri Lanka's High Commissioner to Australia, Admiral Thisara Samarasinghe.

The minister was told details remain sketchy and investigations were continuing in Sri Lanka.

Australian Federal Police are assessing reports and liaising with Sri Lankan authorities.

"The government works closely with Sri Lanka on people smuggling matters, including on disruptions," the minister's spokesman told AAP .

"Minister Bowen was there himself only a several months ago and met with senior members of the Sri Lankan government."

Opposition Immigration spokesman Scott Morrison said the alleged criminal behaviour of the asylum seekers should draw a tough response from the Australian government.

He said the government needed to help Sri Lankan disrupt people smuggling operations.

On Wednesday, police arrested another 35 people heading for Australia in a fishing boat, the officer said.

Sri Lankan authorities say they have detained more than 1,000 people who have tried to leave for Australia illegally this year.

Sri Lankans pay up to $US3,000 ($A2,900) for a place on trawlers which take about two weeks to make the treacherous crossing to Australia.

Meanwhile two boats carrying suspected asylum seekers have been intercepted heading for Australian territory.

Home Affairs Minister Jason Clare said HMAS Hervey Bay intercepted the boat carrying 65 people west of Cocos (Keeling) Islands today.

HMAS Bundaberg intercepted a boat carrying 64 people near Christmas Island this morning.

HMAS Hervey Bay transferred its passengers to Cocos (Keeling) Islands for basic checks.

They will be transferred next to Christmas Island for further security, health and identity checks.

The federal government has warned that people arriving by boat without a visa after August 13 risk being transferred to Nauru or Manus Island under its new offshore processing arrangements.

- with AAP

Originally published as Throat slashed as boat seized in attack