The media mogul had tweeted after the publication of the controversial photos on gossip website TMZ that there is "no such thing as a free press in the UK", and that the "internet makes a mockery of these issues". He then went on to offer to public support for the Prince.
The Independent reported that a source close to News International has claimed that Murdoch personally advised chief executive Tom Mockridge on the issue.
Murdoch reportedly told him: "There is a principle here. I know this is about Leveson but this is humiliating.
"We can't carry on like this. We should run them, do it and say to Leveson, we are doing it for press freedom."
However, the Daily Mail reports that the 84-year-old denied he had been involved in the decision to print the photos, in a Twitter exchange with former deputy prime minister John Prescott.
Murdoch tweeted: "Decision was rightly that of the editor, and I support. I was in Silicon Valley far removed."
The Sun has sparked a media debate with its publication of the photos - despite arguing that it was a 'crucial' test of the country's free press, over 850 members of the public complained about the decision.