In heated exchanges with MPs who were grilling him for a second time about the now-defunct tabloid, the News International chairman instead accused two former executives of keeping him in the dark about the scandal.
Murdoch, 38, was recalled by the parliamentary media committee to explain apparent discrepancies in the evidence he gave during the previous hearing in July alongside his father, media mogul Rupert Murdoch.
Labour MP Tom Watson stunned the hearing on Thursday by accusing News International of being bound by a pact of "omerta", the Italian mafia's code of silence.
James Murdoch dismissed the comparison as "offensive" but Watson pressed on, saying "Mr. Murdoch, you must be the first mafia boss in history who did not know he was running a criminal enterprise."
The comment prompted gasps in the packed committee room and Murdoch appeared briefly taken aback, before replying: "Mr Watson, please. I think that's inappropriate."
The 168-year-old News of the World was shut down in July after it emerged it had hacked into the voicemails of murdered teenager Milly Dowler.
Murdoch fended off repeated questions about accusations by former News of the World editor Colin Myler and legal chief Tom Crone, who said he lied about whether he had seen a "smoking gun" email about the extent of hacking.
He admitted that he was told of the email at a meeting in 2008, which was aimed at deciding a payout for hacking victim Gordon Taylor, head of the Professional Footballers' Association.
But he repeatedly denied actually being shown the so-called "for Neville" message -- which which was apparently meant for chief reporter Neville Thurlbeck -- or realising it indicated hacking was widespread.
He then tried to shift the blame, saying that Myler and Crone had themselves "misled" parliament when they suggested Murdoch knew about the email's contents, and that they had failed to give him necessary details.
Crone later issued a statement accusing Murdoch of being "disingenuous."
"The simple truth is that he was told by us in 2008 about the damning email and what it meant in terms of wider News of the World involvement," he said.
Committee chairman John Whittingdale said after the hearing that there were "direct contradictions" between Murdoch's evidence and the accounts of Crone and Myler.
Whittingdale also said parliament could impose sanctions if the committee concludes that any of them misled lawmakers, but did not say what they were.
Murdoch meanwhile repeated his apologies for the scandal.
Thurlbeck afterwards said he had compiled a hacking dossier which would back Murdoch's recounting of events.
"It will be good news in a way I think because it will back up his claim that he has been seriously misled by senior executives on the News of the World," he told Channel 4 News.
Damaging new claims in the past week had heaped pressure on the young scion of the Murdoch dynasty, particularly allegations that a private detective hired by the News of the World tracked lawyers of hacking victims.
Murdoch condemned the decision to hire an investigator as "appalling" and said Crone and a second, unnamed, News of the World employee were responsible.
Security was tight for the two-hour and 37-minute hearing in a building adjoining the Houses of Parliament, after the Murdochs' previous appearance was disrupted when a man flung a foam pie into Rupert's face.
James Murdoch's position at his father's US-based News Corporation empire has appeared increasingly shaky, and there are doubts over whether he will be re-elected chairman of pay TV-giant BSkyB at an annual general meeting at the end of the month.
In his first appearance at the committee on July 19, James Murdoch maintained he had believed until last year that hacking was carried out by just one "rogue reporter", former royal editor Clive Goodman.
Goodman was jailed in 2007 along with private detective Glenn Mulcaire after they admitted hacking into royal aides' phones, after which police closed the hacking probe until January this year when it was revived amid new claims.
After the revelations about Milly Dowler in July, two of Rupert Murdoch's most trusted executives quit, as well as Britain's top police officer and one of his deputies following criticism of the original probe.
