The Parliament shall, subject to this Constitution, have power to make laws for the peace, order, and good government of the Commonwealth with respect to: … the naval and military defense of the Commonwealth and of the several States, and the control of the forces to execute and maintain the laws of the Commonwealth …That is the clause of the constitution I was referring to. The Parliament is not powerless against the states if it chooses to act.
The section you're quoting only allows the Commonwealth to enforce Commonwealth laws. It doesn't allow it to overrule state laws. If it was, why would Australia have states at all - we'd only need a federal government because it could make all the laws. That's now Australia was set up.
Take a look at this link - in particular the first part of it.
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