Further to my previous post, the following is from the ATO web site:
If you have the relevant records (for example, share certificates), you may be able to identify which particular shares or units you have disposed of. In other cases, the Commissioner will accept your selection of the identity of shares disposed of.
Alternatively, you may wish to use a 'first in, first out' basis where you treat the first shares or units you bought as being the first you disposed of.
In limited circumstances, we will also accept an average cost method to determine the cost of the shares disposed of. You can only use this average cost method when:
the shares are in the same company
the shares are acquired on the same day
the shares have identical rights and obligations
you are not required to use market value for cost base purposes.