The agency said the problems on the Greek shipowner's 33,300-dwt Apellis (built 2010) were uncovered during an inspection at the grain jetty in Esperance in Western Australia.
The Panama-flagged ship is on charter to US-based Hudson Shipping Lines.
AMSA said the vessel's seafarers were not being repatriated or receiving monthly salary as required by employment agreements.
One crew member on the vessel was found to be working beyond medical restrictions, and there was no working washing machine in the crew laundry, among other deficiencies alleged by the agency.
