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If someone is flying from the US to a city in Australia and has to take a connecting flight in a different state, e.g. flying from Dallas to Darwin in the Northern Territory, and they have to take a connection in Sydney, New South Wales, then is the custom check only at the Port Of Entry, e.g. Sydney? Or since different states in Australia have different Customs rules, will there be a need to clear Customs in Darwin too?

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Different states do not have different Customs rules. There are some special zones around Australia but those aren't enforced by Customs. When catching a connecting flight it depends on whether your connection is departing from the international or domestic terminals.

Unlike many or all US airports, Australian airports that regularly service international flights have their international operations completely separated from their domestic operations. This means that if the connection you're intending to catch, e.g. Sydney to Darwin, is leaving from the international terminal you will only have to clear Customs upon arrival in Darwin. However if it's leaving from the domestic terminal, as is most likely the case, you have to clear Customs in Sydney. You will only clear Customs once.

When dealing with the special zones regarding transporting of fruit, etc, within Australia, there will be prompts and bins to discard the foodstuffs on your way out of the airport but there will not be Customs-style checks to verify you don't actually have any.

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Otherwise correct, but I think you've reversed the order of the OP's flights: he's flying first into Darwin, where he'll most probably clear customs, and then connecting to Sydney. –  jpatokal Jan 16 at 22:28
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I don't think so, as that's not how I read it - he's saying he's flying from Dallas to Darwin, and as part of that he has to catch a connection from Sydney. That order also makes a lot more sense when you consider that Dallas to Sydney is a direct flight, whereas to get from Dallas to Darwin without going through Sydney is probably a three hop flight or more. –  dlanod Jan 16 at 23:03
    
Oops! You're right, I read "connection in" as "connection to". –  jpatokal Jan 16 at 23:46
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There can sometimes be sniffer dogs to verify you're not carrying fruit and vegetables, but that's as close to an international-entry customs zone as you'll get. –  David M Jan 22 at 22:10
    
@DavidM I had a feeling I've seen them in the past in domestic terminals but I wasn't sure so didn't want to mislead. Good to see confirmation. –  dlanod Jan 23 at 0:00
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