The notes do cost more to produce, but the extra durability means that they last about 4 times as long (from memory) in circulation, so overall the cost difference is marginal for the government, but is an additional deterrent for counterfeiters.
[1] http://en.wikipedia.org/wiki/Polymer_banknote [2] http://www.rba.gov.au/banknotes/counterfeit/index.html