There aren't any guidelines to my knowledge. You select the shares to sell based on what is the most advantageous to you. However, you must keep good records in case you are audited.
An example:
If I have 1000 shares in ABC bought in Nov 2019 @ $10/share and another 1000 bought in Nov 2020 also at $10/share. They are now trading @ $15/share. I have a capital loss from other share sales either this year or carried forward from last year of $5,000.
I now want to buy a $16,000 car and decide to sell 1000 shares in ABC to help with the purchase.
In this case I would sell the most recent 1000 shares bought, not the first. These will have a non-discountable capital gain of $5,000.
The way the CGT system works, the $5,000 loss from the other sales will be applied against this capital gain leaving no gain for the year and no carry forward loss into next year. I will still have the other 1000 shares of ABC which are discountable.
If I followed FIFO, then the $5,000 loss would be applied against the $5,000 discountable gain from the first lot of shares. As the loss is applied before the discount is calculated, then I end up as before with no gain for the year and no carry forward loss into next year. However, I still have the second batch of ABC on hand, but as they were bought just last month, they do not qualify for the discount. If I wait until Nov 2021, then they will be entitled to the discount, but what if I must sell them before then for some reason. I will be taxed on the full gain rather than the discounted gain.
So this is one example of where adopting FIFO is not to your advantage and the tax office does not require you to do so.
As I mentioned before, you could also have sold 500, say, from the first batch and 500 from the second batch, if that is the most advantageous to you, though I can't come up with a ready example of where that might be the case.
