Peter Sharp, originally from the Shetland Islands, faces 162 counts of manslaughter by criminal negligence after the loss of one of his vessels off Morobe Province last February.
It is thought the death toll is probably higher as a number of children under three were not recorded on the ship's manifest.
The ferry owner is accused of knowingly sending the Rabaul Queen to sea in an unseaworthy state.
The 69-year-old, who has lived in the region for a number of years, was ordered to surrender his British passport before appearing in court in Papua New Guinea this week.
Mr Sharp has blamed a rogue wave pattern for causing the ferry to capsize.