The News Corp chairman and chief executive, who
received a cash bonus of $12.5m (£7.7m) for the last financial year, made the admission in the company's annual report, reports The Australian.
"As has been widely publicised, our company has received a major black eye from the phone hacking scandal at our News of the World newspaper in the UK," he wrote.
"As I said at a parliamentary hearing, this episode has been the most humbling of my career.
"Let me be clear: the behaviour carried out by some employees of News of the World is unacceptable and does not represent who we are as a company. It went against everything that I stand for."
Murdoch admitted that the various investigations and legal cases resulting from the phone hacking scandal "could damage our reputation and might impair our ability to conduct our business".
He said that news director Joel Klein, a former official at the US Justice Department, has been given the job of "getting to the bottom of the matter".
Murdoch also expressed his belief that he can "put things right", after he pledged last month to do "whatever is necessary" to prevent a repeat of the phone hacking scandal that resulted in the closure of the News of the World.
"We are better positioned financially and operationally than we have ever been," he said, after News Corp reported operating income of $4.98bn (£3.08bn) in the 12 months to the end of June.
"I realise the current flavour of the day is economic pessimism, and it is clear that Europe in particular is in the midst of a period of extreme volatility.
"However, I am optimistic about the future because I believe that News Corporation... will continue to shape it."