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.