International Transport Federation co-ordinator Dean Summers said the Filipino crewman had gone missing from the vessel Sage Sagittarius at the weekend in the Timor Sea.
The ship had been scheduled to load in Newcastle next week but was diverted by authorities and was expected to dock today in Port Kembla.
The Australian Federal Police said last night they were investigating the case and had been alerted to problems on the ship on Sunday by the Australian Maritime Safety Authority.
Mr Summers said the ship’s owners had flown private security guards and company representatives to the ship by helicopter from Brisbane.
Until then, most of the 21-man crew had apparently been ‘‘holed up in a cabin, fearing for their safety’’.
Mr Summers said the ship had ‘‘done a search pattern’’ to look for the missing seaman and alerted the Australian authorities when it couldn’t find him.
‘‘It’s been suggested to us that the man met his death through foul play because he was going to come to us with an allegation of poor pay and conditions on the ship,’’ Mr Summers said.
‘‘We don’t know for sure, but that’s what we were told early on.’’
The federation is an internationally recognised trade union body that fights for seafarers’ rights and which works to expose so-called ‘‘ships of shame’’.
Mr Summers said the Sage Sagittarius was a ‘‘flag of convenience’’ vessel registered in Panama and owned by Japanese interests.
It was a regular visitor to Newcastle.
Newcastle Port Corporation shipping movements were last night still showing it as docking at the Kooragang Number 6 berth next Thursday.
Mr Summers said the federation was investigating the situation through its London office.
Although the ship, which was built in 2001, had an agreement with the federation to pay its crews at least the minimum standard of about $1350 a month, it appeared there had been problems on board.