Hang on a moment peeps, two different types of tax are being discussed...
As posted above, if you are working and the MECIR will improve your skills with your current employer, you can claim it. Check the ATO website under 'airline pilots' for details (covers all pilots). I have done so, accountant okayed it, and three years later still haven't heard anything from the ATO (but i'm still hanging on to receipts just in case). Nice little $4000 bonus it was.
Paying GST during training is a totally different kettle of fish all together. If it is part of a 150hr CPL course, then you don't have to pay GST. If you have a CPL or are doing the 200hr CPL course you need to pay GST. I have seen two pilots ask for a private ruling on this and both didn't come back in their favour.