He quit News International's (NI) three major publishing houses – News Corp Investments, News International Group and Times Newspaper Holdings.
NI would not confirm details of the US "small subsidiary boards" from which he had resigned.
A spokesperson for the media giant said that Murdoch would remain committed to his role as chief executive of entertainment and reduce his duties to chairman of the publishing business when the conglomerate splits.
She added: "Murdoch remains closely involved with the business."
In June, the company announced that it was to split its publishing operations from the film and television business, to be formed of broadcasters including US-based Fox News channel and the UK's BSKYB. HarperCollins will join titles such as The Sun and The Times in the newspaper and book publishing unit.
The spokesperson said: "Newspaper publishing is always going to be the main focus for News Corp. This is nothing more than a corporate housecleaning exercise prior to the company split."
NI recently pulled its titles from Johnston Press’ Portsmouth and Dinnington facilities in a £30m buy-out five years into a 15-year contract.
The spokesperson said: "The contract was terminated to enable News International to rearrange its contractual agreements and use its in-house capacity."
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