Whomever deposited the funds into the account. I.e. the ATO directly, or if the ATO paid the refund to your agent and your agent deposited it into the account contact them. They should be able to reverse the transaction through their bank.
Yes you are correct, stealing mail before delivery and opening mail that you are not authorised to open is mail tampering and is a Commonwealth offence. In that case you could also contact the Federal Police.