Australian Government information on how to find your way through the Byzantine and daunting regulations dealing withcruising through Australian waters. This includes the law that yachts must announce their arrival at least 96 hours in advance. 

See  the account by Will Cloud of the reaction of the Australian authorities if you fail to do so:

I HAD entered Australian waters at Cairns and been cruising up the east coast for over a month before reaching Darwin. The Darwin authorities in charge of controlling the striped mussel invasion required my boat’s through-hulls to be sealed and a hospital grade disinfectant poured into each sink, toilet and engine opening. The boat was then required to sit undisturbed for 18 hours before being allowed entry to any of the water lock sealed marinas in Darwin.

The real hassle was with Customs on entry to Australia at Cairns from Vanuatu. Our four day advance notice (required of all vessels) was not given in time. When I was two days out I contacted the marina at Cairns by email and asked if they would take care of the formalities. They agreed. At the time we had been under the impression that two days notice was the requirement. While still a few hours outside Australian waters I spoke with Australian Customs on VHF and they informed me of the four day requirement. I responded that I could wait outside the reef for two more days, but that I was low on fuel with 20kn trade winds making the reef a lee shore. Customs advised me to come in and we could then discuss the issue. At dock, Customs as well as Immigration and the Agricultural Inspectors spent an hour clearing us in and all the forms were signed. I was officially in Australia.

Then the Customs agent I had spoken with earlier on VHF informed me that the investigation would now begin and anything I said could be used against me in a court of law. I immediately lodged a complaint that the procedure was improper. I had already been questioned for an hour without any notice of court action and I had obtained official permission to enter Australian waters from the agent herself prior to the usual four day requirement. She proceeded nevertheless and placed the boat under seizure with orders not to leave the dock until the issue was resolved. She didn’t call it seizure. This is my and most peoples’ interpretation of the situation.

The next day another Customs agent came down and presented me with a notice that I and my boat would be released, but we were being added to the list of boats who have been warned. Apparently over half of the boats entering Australia end up on this list, which sets us up for heavy fines if it happens again. An American boat was fined several thousand dollars.

I told him I was very concerned that vessels in distress would be tempted to remain outside Australian waters to fulfil the four day requirement, because they could not believe Australian Customs would honour an agreement to allow then in earlier. They could cause danger to themselves and other boats.

The Customs agent became angry and tossed the warning papers at me and said that I could accept the decision or go to court. I told him I would need to speak to the Director of the local Customs office. I reasoned with him that the coastline of Australia is huge and Customs is never staffed fully to protect Australia without the cooperation of local citizens and visitors alike to report suspicious activity. I and my crew were in complete agreement with the need to follow all the rules and support the role of Customs. I just wanted the application of the rules to be fair and consistent.

Finally we got our cruising permit and the rest of my time in Australia was wonderful. I particularly thanked the Customs pilots who flew over us twice a day and requested identification via VHF.