Two weeks later, as the Japanese-owned, Panama-flagged coal carrier Sage Sagittarius was about to enter Newcastle harbour, the chief engineer was killed by an 11-metre fall from one deck to another.

A month after that, when the ship had docked in Japan, a safety superintendent was crushed to death by a conveyor belt. This third incident falls beyond the scope of the NSW Coroner's Court inquest at Glebe.

The chief cook and chief engineer on board the ship that was bound for Australia are highly likely to have met with foul play, the court has heard.

"At the very time of the disappearance and the death, there was intense personal conflict and mutual mistrust among the crew," counsel assisting the inquest, Philip Strickland, said on Thursday.

The court was told the ship's captain, Venancio Salas, had been accused of physically assaulting crew and pressuring them to buy guns from his contacts. Mr Strickland said there were competing versions of events among the crew, as well as a "culture of silence".

The Filipino cook Cesar Llanto, 42, disappeared about 8am on April 30, 2012, as the ship was passing through the Coral Sea, north of Queensland. Tensions between the captain and one of Mr Llanto's staff had been intensifying in the days before the disappearance, the court heard.

According to an anonymous crew member, the captain asked all crew to throw out gun brochures because he thought Mr Llanto's staff member would report him to authorities once the ship regained mobile reception. Mr Llanto either supported or opposed the reporting of his captain, according to different stories.

Mr Llanto's widow, Nelia, told the court via video link that her husband had been happy and healthy and rarely took risks.

"I pity my children and please have pity on them as well," she said. "I just want to know the full truth."

The ship docked at Port Kembla where it was investigated by members of the Australian Federal Police, then continued on to Newcastle.

Hector Collado, a 57-year-old engineer from the Philippines, died about 8am on September 14, just before he was due to disembark at Newcastle. The court heard Mr Collado had been "deeply distressed" by the cook's death. He allegedly visited Captain Salas a few days before his own death, telling him that there was a threat to his life.

Counsel assisting said the engineer's widow had not wanted to co-operate with an investigation or inquest, expressing fear and disconnecting her landline phone.

Mr Collado was found with a curved wound to his head. "There is no reasonable explanation at this stage about how he could have sustained that injury accidentally," Mr Strickland said.

Forensic pathologist Dr Brian Beer told the court the death was suspicious because the head injury appeared unrelated to the injuries from the fall.

The inquest continues.