The State Services Commission released a report today into his handling of the breach of Budget information from Treasury's website, describing it as "clumsy" and unreasonable.
It also criticised him for not taking responsibility for the incident.
In a statement this afternoon, Mr Makhlouf has apologised for not keeping the information secure.
"Mr Ombler's investigation was conducted thoroughly and fairly. I have read the report carefully and encourage others to do so. I apologise that Budget information was not kept secure."
However, he said the report confirmed he acted in good faith and without political bias.
"It also confirms that I acted reasonably, other than in my descriptions of the incident. I am pleased that my honesty and integrity are not in question."
He said a separate inquiry would look at exactly how the Budget information was accessed, and how to stop it from happening again.
Mr Makhlouf officially finishes at the end of this week before heading off to take up the job as the head of Ireland's central bank.
Dr Caralee McLiesh, managing director at Technical and Further Education New South Wales, will succeed him and starts in September.
