The Transport Accident Investigation Commission has launched an inquiry into the fire on board the Hong Kong-registered cargo ship Kokopo Chief berthed at the Port of Tauranga.
A spokesperson from the commission said two investigators were expected to arrive at the scene this afternoon to begin working to establish the cause of the fire.
Smoke was seen coming from the hold of the ship at about midnight, and the ship's crew activated the fire extinguishers and advised emergency services.
More than 70 firefighters responded to the blaze, located below the decks, on the vessel which was carrying 650 tonnes of dressed timber in the main cargo area.
Deck containers with dangerous goods were removed, and there were no reported injuries.
All 48 containers on board the ship were removed shortly before 6am today.
Fire crews on a tugboat assisted in removing the ship's hold cover to check how far the fire had spread and if it was out.
Northern fire communications shift manager Colin Underdown earlier said 16 crews had responded to the blaze after high temperatures set off an alarm at 1am today .
The ship's CO2 suppression system had activated, he said.
Mr Underdown said firefighters and ship management lifted the hatch covers at 10am to check if the CO2 discharge had put the fire out.
Port of Tauranga chief executive Mark Cairns confirmed the fire was out when the hatches were opened at 10am yesterday (Sunday), and port stevedores then began to remove the fire-damaged timber.
He understood there was no structural damage to the vessel.
Mr Cairns said the ship would remain in port for a couple of days while the CO2 suppression system was recharged.
Tauranga, Mount Maunganui, and Greerton fire crews responded as well as two crews from Rotorua, a command unit and aerial appliance.
Volunteer crews from Katikati, Te Puke, Omokoroa, Maketu and Papamoa, had also responded to the incident, he said.
Specialised breathing equipment had also been brought in from Auckland, and another fire truck had come from Ngaruawahia.
Some of the out-of-town fire crews were used as backup support at the Western Bay of Plenty fire stations.
The Transport Accident Investigation Commission was unable to comment further on the incident while the inquiry was ongoing, its spokesperson said.
The more than 158m long Kokopo Chief, which is registered under a Hong Kong flag and built in 1991, arrived in port on September 21.