When do I lodge my Quarantine Declaration for a container that is arriving to one port and then transhipped to another port?

You should lodge your container information, including the quarantine declaration, with MAF prior to the vessel arriving in New Zealand. This is to allow the necessary risk analysis to be done on your container before arrival, to minimize delays in New Zealand. If you plan to lodge your Customs import entry late (e.g. after arrival of the vessel), you must still lodge details of the container with MAF (use the dedicated Customs ECI report, or make a manual application) before it is moved from the wharf.

At some ports with documented, MAF-approved equivalent biosecurity systems in place, otherwise low-risk containers may be transported from the wharf to an inland facility prior to presentation of the quarantine declaration. But you should still plan to lodge all information with MAF as early as possible, to avoid delays between unloading and transport from the wharf.