Mr Murdoch was put on the spot by Liverpool Walton MP Steve Rotheram as he gave evidence about the News of the World phone-hacking scandal to the Commons Culture, Media and Sport Committee.
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He accepted that it was 'wrong' for The Sun to have printed allegations about the behaviour of Liverpool fans under the headline 'The Truth'.
Mr Murdoch told the committee: 'I would like to add my full apology for the wrong coverage of that affair. I would like to add my voice to the successive editors of The Sun and chief executives of News International who since that incident have apologised.
'It was wrong to do so. It was 22 years ago and I was far away and a much younger person and had no involvement or proximity to it, but I have since looked at it and I am aware of the concerns and the hurt it caused and it is something we are very sorry for, and I am as well.'
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Mr Rotheram suggested that the lack of serious repercussions for The Sun of printing the story may have encouraged a sense at News International that the company was 'untouchable'.
'Did the fact that The Sun got away with telling outrageous lies in 1989 lead News International into believing they could do whatever they wanted without reproach?' asked the Labour MP.
'Did the lack of appropriate corporate governance give a false sense of security that News International was untouchable?'
Grilling: Steve Rotheram quizzed James Murdoch
Mr Murdoch responded: 'I don't think there has been - certainly not in my experience of the company - a sense that anyone is untouchable.
'What we want to be is the business we aspire to be, where we are doing the good work of serious journalism and serious creative endeavour.'
Mr Rotheram pressed Mr Murdoch to pledge that The Sun would be closed down, as the News of the World was, if evidence emerged to prove its reporters were involved in phone-hacking.
TheNews International executive chairman replied: 'I think it is importantto not prejudge the outcome of any investigation. Nor is it appropriateto prejudge any actions the company might take.
'Idon't think we can rule - and I shouldn't rule - any corporate reactionto wrong-doing out. That will be a decision taken at the time given whatever is out there.'
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