The Australian-born media mogul made the move last week, according to a spokesman for News International, a British arm of News Corp.
It's not clear who will be CEO of the publishing company, which would be less than one-third the size of its counterpart.
The News International spokesman on Saturday played down Murdoch's boards resignation, calling it "nothing more than a corporate house-cleaning exercise prior to the company split."
News Corp., a Murdoch-controlled media conglomerate, is expected to be divided in the next 12 months. The split comes after some of its U.K.-based newspapers were thrust to the center of a recent phone-hacking scandal.
His British operations have remained under intense scrutiny after revelations of widespread phone hacking, which included celebrities and public officials, by people working for his newspapers.
The controversy prompted News Corp. to shut down its venerable British tabloid, News of the World, last year, and preceded a decision to withdraw a multi-billion-dollar bid to take over British Sky Broadcasting.
The coming split would separate operations like 20th Century Fox film studio, Fox broadcast network and Fox News Channel from the firm's newspapers holdings such as Britain's The Sun, the London Times and the London Sunday Times.
News Corp.'s American media holdings include The Wall Street Journal, the New York Post and Barron's. Its book publishing assets include such companies as HarperCollins.