Mr Huntington said the load would take five or six days to unload with herring going to most of the tuna companies.
This year's load was slightly smaller than last year's delivery, but Mr Huntington said this year a second ship would arrive in February with several thousand tonnes of pilchards caught off the coast of North Africa and delivered from Spain.
These pilchards were also of a high quality and would be very palatable for the tuna, he said.
Organising the unloading was freight forwarding and logistics company Power House International, which hired about 70 local P&O Ports workers.
The herring are classified as a "specified species" by Biosecurity Australia because of concerns raised about the spread of fish disease viral haemorrhagic septicaemia or VHSV.
Restrictions from farmers prevent them from using the herring between 1 June and 30 November when the chances for the water temperatures being below 15 degrees are greatest, which are the conditions where the disease could spread to local stocks.
Restrictions on other imported baitfish such as pilchards and mackerel also are in place.
Companies storing and thawing imported bait have also been required to place quarantine signs around their properties, according to a Australian Quarantine and Inspection Service spokeswoman.
Tuna industry spokesman Brian Jeffriess said the restrictions on the use of important imported bait such as herring were damaging to the industry and efforts where being made to relax the restrictions because there could be instances during the upcoming season where no suitable bait would be available.