The chief cook, Cesar Llanto, 42, disappeared overboard from the MV Sage Sagittarius on August 30, 2012, as it approached Australian waters in the Coral Sea en route to Newcastle.

Two weeks later, his friend, chief engineer Hector Collado, 55, was killed while the ship was moored at Newcastle Harbour.

Following an inquest spanning more than 18 months, coroner Sharon Freund found on Wednesday that both men were killed by an unknown person or persons.

A third man, Kosaku Monji, 37, a Japanese superintendent, was crushed to death in a conveyer belt as the Sage Sagittarius docked in Japan in October 2012, but his death did not fall under the coroner's jurisdiction.

Mr Monji had come aboard the ship on September 3, 2012, to investigate Mr Llanto's disappearance and to ensure the safety of the crew.

The vessel, owned by a Japanese company, was operating under the flag of Panama, using a system known as a "flag of convenience". Such a practice involves registering a ship in a country other than that of the ship's owner to avoid the laws of the owner's country.

Outside the Coroner's Court in Glebe, Dean Summers, the national co-ordinator for the International Transport Workers Federation, said the flag of convenience system made workers vulnerable.

"Today the coroner has confirmed that, on board the Sage Sagittarius, a flag of convenience ship, sailing to and from Australia, there has been a double murder.

"This was a murder ship. The Sage Sagittarius - flag of convenience registered in Panama - was a murder ship, and two men have lost their lives, two families have lost their breadwinners, four children have lost their fathers," Mr Summers said.

"This is a terrible indictment of the flag of convenience system."

The inquest heard there was "intense conflict and mistrust among the crew" on board and some of the crew, including Mr Llanto, were planning to report the captain, Venancio Salas, 40, to authorities for alleged physical assaults and maltreatment.

A culture of "silence and blacklisting" and "harassment and bullying" existed, particularly of messman Jessie Martinez because of his junior status and homosexuality. Mr Martinez was assaulted by Captain Salas on three occasions.

Captain Salas also sold guns on board, collecting and sending thousands of dollars to the Philippines and taking a small commission.

Ms Freund said Mr Llanto was either thrown overboard or killed and his body disposed of later. As his body has never been recovered, she made an open finding as to the cause of his death.

Mr Collado was struck over the head with a weapon or instrument and he was either thrown or fell to his death from the second to the fourth deck. The cause of death was multiple injuries.

The inquest was plagued with difficulties, including the reluctance of most of the crew to co-operate with authorities. Investigators found some of the crew were scared and intimidated by the three deaths and it was abundantly clear a number of them did not disclose everything they knew to authorities.

Further, the Australian Federal Police had jurisdiction over Mr Llanto's disappearance while the NSW Police had carriage of Mr Collado's death

The Sage Sagittarius carries coal between Australia and Japan and is owned by Nippon Yusen Kabushiki Kaisha Line, one of the biggest shipping companies in the world with revenue of more than $20 billion.

When it departed Japan for Newcastle in August 2012, it carried 25 Filipino crew members.

In her findings, Ms Freund said a landmark report Ships of Shame was published following a Commonwealth parliamentary inquiry two decades ago, yet many of the issues remain.

There are significant practical impediments to investigating suspected lawlessness on a foreign-flagged vessel, the report found, including crew members' fear that speaking out will affect their ability to get work.

Ms Freund made five recommendations, such as the establishment of a permanent standing group comprising the NSW Police, federal police, Australian Maritime Safety Authority and Australian Transport Safety Bureau to deal with deaths on board international vessels bound for or in Australian waters.

In a statement, NYK said: "We need time to examine the Coroner's findings in detail before commenting further. What we can say is the welfare of our ships' crews is always of the utmost concern to us and we will continue to take all steps to provide a safe working environment."