During questioning today by MPs on the Commons culture, media and sport select committee, Tom Watson MP asked Murdoch if he was aware of the mafia term 'omerta' - the code of silence.
Watson suggested that News International had behaved in a similar fashion during the phone hacking scandal, but Murdoch said the claim was "offensive and untrue".
The MP also told Murdoch, who has consistently denied any knowledge of the scale of phone hacking at the publisher, that he "must be the first mafia boss in history who didn't know he was running a criminal enterprise".
However, the News Corporation executive replied: "Mr Watson, please, I don't think that is appropriate."
Murdoch, the executive chairman of News International, told MPs that he was not shown a crucial email suggesting that illegal practices at the defunct Sunday tabloid went beyond one "rogue reporter" - referring to royal editor Clive Goodman, who was jailed for phone hacking in 2007.
He admitted that he was told about the document - known as the "for Neville" email - but had not been shown it before approving a major settlement payment to Professional Footballers' Association chief executive Gordon Taylor in 2008.
Answering questions from the committee for the second time, the son of Rupert Murdoch gave a polished performance, but faced some seriously uncomfortable moments.
Murdoch was consistently pushed as to why he was not "more curious" over the details surrounding the payment to Taylor, which is thought to have amounted to more than £700,000.
The MPs asked why he did not question the fact that Taylor was involved in the football industry rather than the royal family, seemingly showing that hacking went beyond Goodman. However, Murdoch was able to brush off the questions.
Murdoch said that he "disputed vigorously" Myler and Crone's account of a meeting in June 2008 to discuss the legal claim of Taylor, who is understood to have obtained a transcript of messages taken from his phone by News of the World journalists.
Murdoch said: "The nature of the so-called 'for Neville' email... any wider spread of evidence or suspicion of wider spread wrongdoing - none of these things were mentioned to me."
However, he added: "I was given a set of information that this was a case [with Taylor]. It was an old matter, it was the same [jailed private investigator] Glenn Mulcaire who has been convicted. I was told there was a piece of evidence that the company would lose the case."
Referring to Myler and Crone, Murdoch said that the committee had been given evidence by "people without full possession of the facts", and insisted that his own testimony had "been consistent" with the knowledge he had at that time.
Murdoch also denied seeing a legal counsel's opinion, by Michael Silverleaf QC, which warned in June 2008 of a "culture of illegal information access" at the media group involving "at least three" journalists.
Asked if he had misled the committee in his evidence, Murdoch replied: "No, I did not."
Murdoch also said that the whole of News Corporation had been "humbled" by the hacking scandal, echoing the statements made by Rupert Murdoch to the MPs in July.
"I have had some time to reflect on these events, and it's appropriate to reflect. The whole company is humbled. What I have to do is understand why the company has not," said James Murdoch.
He also claimed that the firm has worked to "improve the structures and leadership across all the operating companies so these things don't happen, because they are something I am not very happy about".
Murdoch denied suggestion that he had been "incompetent" and said that News International is a small part of the News Corp Europe operation, meaning he relies on senior managers to "behave in a certain way". However, he also denied that the company had been guilty of "wilful blindness" in the phone hacking scandal.
Reports have suggested that more than 150 high-profile public figures could have been followed by the private investigator, including committee member Tom Watson, who this week claimed that News International's surveillance tactics were akin to the Soviet era.
Murdoch said that the decision by Crone to hire the private investigator to run surveillance on Lewis and Harris was "appalling", and "something that I would never condone and the company should never condone".
He also admitted that he was recently made aware of surveillance of Watson and other members of the culture committee, saying that it was "not acceptable" and apologised directly to the MPs.
Murdoch also refused to rule out closing The Sun should there be revelations about phone hacking at the tabloid newspaper. A reporter from The Sun was arrested last week on suspicion of phone hacking and police have said they are investigating 300 million emails from the News International paper.