Australian Customs and Border Protection officials raided a coal-carrying vessel 13 times in the three years before three of its crew were killed in suspicious circumstances.

Four Corners has also established that four of the Sage Sagittarius' crew, including its captain, had been flagged on a border protection database.

The program delves into the mystery of the vessel dubbed the ship of death, revealing the inside story of the 2012 voyage when the deaths occurred, using the crew's own accounts.

The Sage Sagittarius was last week at the centre of a coronial inquest in New South Wales where evidence was heard that the deaths may have been the result of foul play.

Deaths aboard Sage Sagittarius Name: Cesar Llanto Age: 42 Nationality: Filipino Occupation: Chief Cook Date of death: August 30, 2012 Location of death: Coral Sea, 450 nautical miles NE of Cairns Name: Hector Collado Age: 55 Nationality: Filipino Occupation: Chief Engineer Date of death: September 14, 2012 Location of death: Port of Newcastle Name: Kosaku Monji Age: 37 Nationality: Japanese Occupation: Superintendent Date of death: October 6, 2012 Location of death: Port Of Kudamatsu, Japan

The ship's captain appeared at the inquest and was asked if he had any information.

He denied any involvement in the deaths.

Other crew members are expected to be called to give evidence at the inquest later in the year.

The Australian Customs Service refused to say why it took an interest in the ship, but said it used a "risk-based approach" to detect illegal activity, and "clearance activities" aboard the ship were for routine reasons.

But a former maritime investigator believes the pattern of raids may point to suspicious activity on board.

Michael Squires, a former investigator with the Australian Transport Safety Bureau (ATSB), engaged by Four Corners to examine evidence, said the attention by Customs suggested something may have been amiss onboard.

"It may be that some of the crew members have some previous history of attempting to bring things in or take things out, but certainly the ship had been flagged by the authorities for more than routine observation," he said.

The deaths took place over six weeks on one of the ship's regular coal routes between the southern Japanese port city of Kudamatsu, and Newcastle in New South Wales.

The first death occurred around 840 kilometres off the coast of Queensland, when 42-year-old chief cook Cesar Llanto disappeared on the morning of August 30, 2012.

The second death occurred about two weeks later, after 55-year-old chief engineer Hector Collado plummeted 12 metres down an engineering shaft after a blow to the back of the head.

The third death was 37-year-old Kosaku Monji, a superintendent at the ship's Japanese operator, Nippon Yusen Kaisha Line.

He was entangled and then crushed by the ship's large unloading rollers while the ship was berthed in Japan during the early morning of October 6, 2012.

Mr Monji's father Shuzo Monji told Four Corners he was unaware there had been two suspicious deaths during the two weeks before his son died.

His son's death was investigated by the Japanese Japan Transport Safety Board which found it was "probable" the death was an accident, but added that it was not possible to determine the true cause "because there were no witnesses of the accident".

Speaking through an interpreter, he said he did not want to consider his son's death may have been suspicious.

"I really want to separate the death of Kosaku as being part of the murder," he said.

Asked whether the company should have told him about the other deaths he replied: "I do not really want to answer that question."

Watch Four Corners: Ship of Death on ABC iView.